Amber - Science topic
A yellowish fossil resin, the gum of several species of coniferous trees, found in the alluvial deposits of northeastern Germany. It is used in molecular biology in the analysis of organic matter fossilized in amber.
Questions related to Amber
I ran a MD simulation for 30 ns using Amber99ff ILDN for protein forcefield and GAFF for ligand forcefield for GKRP and F1P (PDB: 4BB9) consecutively. However, the result shows that the RMSD Complex fluctuates over time until it reach about 27 ns. Also, the RMSD score varies between 50-100 A which very high RMSD score.
Thank you in advance.
In the 1K1D PDB structure, there is a lysine-carboxylic acid ligand (KCX-150) connected to LEU-149 and ALA-151 by its N and C atoms, respectively. To calculate the parameters of separated hetero groups, I optimize them using the Gaussian package and then calculate them using the AMBER antechamber module.
What is the best way to calculate the parameters of this connected ligand?
I obtained the rmsf graph by using the command line
atomicfluct out rmsf.bfactor @CA byatom bfactor
I have run the MD for 50 ns
Now I want to obtain an ideal graph for publication purpose .
I am attaching the graph below .Plz let me know where to rectify it in command line.
I have a PDB file of a branched polymeric chain, I want to simulate its water solvation using "openMM"
My problem is to find an amber force field to fit that branched chain.
By the way, I have the force field file (XML) which fits the linear polymeric chain (attached)
I am trying to simulate a glycoprotein, but the charmm-gui generated glycoproteins are of no use. Hence, I need to use glycam forcefeild for this, but it is available only for Amber and i cannot find one for gromacs, can anyone help me with this?
I am trying to run a QM/MM in Amber on a protein-ligand system. I have looked for tutorials but they don't explain a few things such as how to heat your system and equilibrate it before MD.
Then there are errors in output files. I have run the questions in the list and applied the changes, but the errors still remain. I would appreciate if someone could share their experience on running these for protein-ligand systems.
I just started with MD simulations to find out more about the interaction of a carbohydrate substrate with my enzyme than I can see from simply docking the substrate into the active site.
I followed the Protein-Ligand Complex tutorial (http://www.mdtutorials.com/gmx/complex/index.html) for GROMACS and got a decent looking simulation (as far as I can tell). However, CGenFF says "CGenFF should NOT be used for biological macromolecules! Only use CGenFF for small organic molecules".
So I would like to use the GLYCAM_06j force field to generate a topology for my ligand. I also used the carbohydrate builder from the GLYCAM website (http://glycam.org/tools/molecular-dynamics/oligosaccharide-builder/build-glycan?id=1) to generate my ligand for the docking. I used tleap from AmberTools19 to generate the topology and coordinate files using the following commands:
tleap -f leaprc.GLYCAM_06j-1
> lig = loadpdb ligand.pdb
> saveamberparm lig ligand.prmtop ligand.inpcrd
Running the loadpdb command returned the following:
Loading PDB file: ./ligand.pdb
total atoms in file: 71
Leap added 40 missing atoms according to residue templates:
40 H / lone pairs
Then, I used the acpype.py script (https://github.com/alanwilter/acpype) to convert the amber topology into a GROMACS topology using the following command:
python3 acpype.py -x ligand.inpcrd -p ligand.prmtop -o gmx
After that, I followed the GROMACS tutorial again creating a topol.top and a protein.gro file using pdb2gmx with the amber14sb force field.Then, I including the ligand_GMX.top file into the topol.top file by adding the following after the ";Include Position restraint file" term:
; Include ligand topology
I also added the ligand to the [ molecules ] entry. I copied the coordinates together in a complex.gro file, created a dodecahedron box and added the water molecules. However, when I get to the step to add the ions using the ions.mdp file provided in the tutorial using this command:
gmx grompp -f ions.mdp -c solv.gro -p topol.top
I get the following error:
ERROR 1 [file topol.top, line 35334]:
No default Improper Dih. types
ERROR 2 [file topol.top, line 35454]:
No default Improper Dih. types
Program: gmx grompp, version 2019.4
Source file: src/gromacs/gmxpreprocess/topio.cpp (line 607)
Syntax error - File ligand.top, line 3
Last line read:
'[ defaults ]'
Invalid order for directive defaults
I already found, that I can only have one [ defaults ] entry in my topology and that there is another one in the forcefield.itp file of the amber14sb force field which is included in the topol.top file. If I simply remove the [ defaults ] entry in the ligand.top file, I get the same error for the [ atomtypes ], which is also present in the ffnonbonded.itp file (included in the forcefield.itp file).
I know, that in GLYCAM_06j, the atom types are intentionally different from those in the amber14sb force field. I also thought about including the atomtypes from my ligand topology into the ffnonbonded.itp file from the amber14sb force field, but the columns have different names in these files.
I read through every tutorial and manual I could find to get to this point, but now I seem to be stuck. Could anyone give me some advice on how to solve this problem. Or is my first simulation already sufficient using CGenFF to prepare the ligand (it's either a tetra- or hexamer). If you need any more information to answer this question, please feel free to ask.
Thank you very much in advance!
I'm using PDB file 5IBE protein structure with co-crystallised ligand 69M for molecular dynamic simulation with AMBER. It is a complex protein with a heme cofactor.
For the preparation of parameter for my non-standard residue ligand 69M,
Firstly, I generated a mol2 and frcmod file using Antechamber for the cocrystallized ligand.
After that, I loaded the generated parameter files (mol2, frcmod -missing parameters) into Leap to enable the Leap to recognise my ligand as a unit and saved the ligand's parameters as library, prmtop and rst7 files. After I completed these steps, I was ready to create the topology and coordinate files for my protein with the cocrystallised ligand (5IBE_69M.pdb).
so, first, I ran Tleap,
then, added the script as followed:
source leaprc.proteinff14SB, source leaprc.gaff,
then I loaded frcmod file as loadamberparams 69M.frcmod
load library file as loadoff 69M.lib
then, loaded my protein pdb file as complex = loadpdb 5IBE_69M.pdb
But, at this last step the I was unable to generate toplogy file and couldn't save pdb as 5IBE_69M.prmtop and 5IBE_69M.rst7 files ?
and I got this kind of errors:
Bond: Maximum coordination exceeded on .R<69M 397>.A<01 2> .R<69M 397> .A<H17 43>
ATOMS NOT BONDED : .R<69M 397> .A<01 2> .R<69M 397> .A<H17 43>
FATAL ERROR --------------------------------------------------------------------------------------------
!FATAL: In file [atom .c], line 445
!FATAL: Message: bondAtomProblem found
I have attached the error file here. please have a look at it and let me know the problem. Your small help can be a huge guide for me to keep stepping forward in my work.
Thank you in advance.
In Orca we can do the relaxed or unrelaxed scanning of any particular internal coordinates (bonds, angled, dihedral). But in output after the optimization we get the energy of the total system. How can I derive ab initio potential for a specific type of bond/angle/dihedral from an orca output? So that I shall be able to use it for potential fitting case. I have attached an image for reference.
I am installing amber 18 on the wsl2 ubuntu 20.04. My machine is ASUS AMD RYZEN5.
Previously I had successfully installed amber18 serial and parallel on wsl1 Ubuntu 18.04. No issues were experienced.
I followed the https://www.ovetande.se/software/amber/install/ambertools19-windows10-wsl/ instructions and the serial was installed successfully. Make tests also ran correctly as indicated on the website
To install parallel the command line is
cd $AMBERHOME/AmberTools/src/ wget https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.1.tar.gz tar xvf openmpi-4.0.1.tar.gz ./configure_openmpi -np $4 (I have 4 CPUS) gnu
i get this error:
Setting AMBERHOME to /mnt/d/amber_files/amber18 Architecture/compiler is not supported Usage: ./configure_openmpi [flags] compiler where compiler is one of: gnu (=gcc/gfortran), intel (=icc/ifort), pgi (=pgcc/pgf90) Option flags: -static Create statically linked executables (not recommended for MacOSX) -np Number of processes for parallel Make Note: See http://www.open-mpi.org/software/ompi/v1.6/ for information on how to obtain openmpi.
I checked the gcc, g++ and gfortran installed on my machine. They are versions (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
I am unable to understand what is wrong except, there may be incompatibility with Ubuntu 20.04.
I had similar issues with another machine Ubuntu 20.04 and parallelisation. So I changed the machine.
Did anyone else have the same problem?
I want to understand the idea behind suffix numbers or letters of Force Fields such as AMBER94,AMBER96,AMBER99,AMBER99SB,AMBER99SB-ILDN,AMBER03 ,AMBERGS ,CHARMM22, CHARMM27, CHARMM36, GROMOS 43a1, 43a2, 45a3, 53a5, 53a6 and 54a7 .
So, how these are referred?
I am trying to use AMBER MDGX to generate sulfer dihedral parameters for deprotonated cysteine. I can properly generate conformers and do the QM calculations to get conformer energies and merge my results. However, when I try to do the parameter fitting for the sulfer dihedrals I am receiving following error "Torsion type SH CT CX C marked for optimization but not found". I can successfully generate bond angle parameters for the SH CT CX and the torsions I try to parameterize are included in my topologies. Is there any way to debug my parameter fitting step or generate parameters based on atoms rather than atom types.
I am going to do MD simulation of G4 (quadruplex) DNA with a ligand. Which MD simulation software should be better for this purpose? CHARMM-NAMA, GROMACS or AMBER. Please explain my why?
Hi there, hope so every one is fine. I am running MD simulation using NAMD for 100ns. My job was terminated twice one at 1.7ns and at second at 3.8 Nano seconds due to the insufficient memory. I have noticed that for 1.7ns of run it produces 33GB of data in ".dcd" file as compare to Gromacs, Schrodinger etc.
My question is that why it is producing too much data and is there any other way to tackle this issue.
Your input will help me to get things done as early possible. Thanks.
antechamber -i L11_h.pdb -fi pdb -o L11.mol2 -fo mol2 -c bcc -nc 1
the output is as follows:
Welcome to antechamber 21.0: molecular input file processor.
acdoctor mode is on: check and diagnose problems in the input file.
The atom type is set to gaff; the options available to the -at flag are
gaff, gaff2, amber, bcc, and sybyl.
-- Check Format for pdb File --
-- Check Unusual Elements --
-- Check Open Valences --
-- Check Geometry --
for those bonded
for those not bonded
-- Check Weird Bonds --
-- Check Number of Units --
acdoctor mode has completed checking the input file.
Warning: The assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase PSCUTOFF in define.h and recompile bondtype.c
(be cautious, using a large value of PSCUTOFF (>100) will
significantly increase the computation time).
Info: Total number of electrons: 216; net charge: 1
Running: /home/user/software/amber20/bin/sqm -O -i sqm.in -o sqm.out
I have a question about programs, that will help to perform alchemy calculations with mutation of one type N-terminal amino acid residue into another type N-terminal amino acid residue without adding a cap (pmx is not suitable in this case).
Could you advise something?
Thank you for your time!
Here are the steps I'm taking:
- ABTS solution: 192 mg of ABTS in distilled water to 50 mL. Store this solution in an amber flask. - Potassium persulfate (140 mM): Mix 378.4 mg of the salt with 10 mL of distilled water. Store in the amber flask ABTS*: The day before the experiment mix in another amber flask 5 mL of the ABTS solution with 88 uL of the potassium persulfate and leave it at room temperature for 16 hours.
However, when I dilute the ABTS* with methanol or ethanol, I cannot achieve an absorbance of .700. Rather, the absorbance is 0.04.
I believe the issue might be coming from the potassium persulfate solution I mixed. Here is the potassium persulfate we purchased: https://www.laballey.com/products/potassium-persulfate-crystal-reagent
Hi every body
I want to use molecular dynamics simulation in my researches and for this purpose, I have two following option:
1- NAMD on windows operating system
2- Gromacs or AMBER on Linux operating system
May you give me more information about simulation speed in these options?
Hardware is same in both case.
I am running MD simulations in AMBER software for docked ligand and protein but I am getting bit confused for while running few of them whether to use them or not.
So anyone can give me list of commands of running md in amber which are error free nd directly can be used.
I was running the md simulations using AMBER software. While running the commands for protein after ligand commands do we have to use the docked protein in the command 'complex = loadpdb 1ua7_noh.pdb' or just the protein in the pdb file.
Thanks and Regards
I have prepared the simulation files for a protein-membrane system using CHARMM-GUI membrane builder option. The force field used there is CHARMM36 FF. Can you please tell me which MD simulation software out of NAMD, AMBER and GROMACS is better to run the simulation without any disruptions?
For my thesis, I am investigating the effects of MDA and 4-HNE in seminal plasma in male patients undergoing IVF, and thus determining if certain levels of MDA and 4-HNE effect IVF outcomes. We are measuring MDA using TBARS assay kit (Cayman Chemical #700870), but we are struggling to find the lipid peroxide level (expressed in terms of MDA) normally found in seminal plasma in published literature. The Cayman Chemical protocol states the normal lipid peroxide level in plasma is between 0.26-3.94 μM, but we are hoping to find a range specific to seminal plasma.
Any help would be greatly appreciated!
I was giving tfollowing the commands
tleap source leaprc.protein.ff14SB MOL=loadpdb 1ua7.pdb savepdb MOL 1ua7-amb.pdb MOL2=loadpdb 1ua7-amb.pdb charge MOL2 source leaprc.water.tip3p solvateBox MOL2 TIP3PBOX 10.0 addIons MOL2 K 14 saveamberparm MOL2 1ua7-wat.prmtop 1ua7-wat.inpcrd
After giving the saveamberparm MOL2 1ua7-wat.prmtop 1ua7-wat.inpcrd .prmtop file is not generated.
How to overcome this problem?
Please help me out.
I am using Gromacs to simulate a biomolecule using the family of Amber forcefields.
I have a protein with a substrate, metals and their coordination centres, and a drug molecule. Parameters for the drug molecule were derived using ANTECHAMBER, and the coordination centre and metals were parameterised using QM calculations and then converted into AMBER force and topology files. Everything was then converted into a Gromacs format.
This is fine until I need to mutate a single residue in the protein. Due to all the numbering etc., I would probably need to go all the way back to using MCPY.py to fit the QM parameters to the modified protein. It is not complicated work, just long and easy to make mistakes.
What are the best strategies to modify a single GLU -> GLN [replaces the sidechain terminus -C(=O)(OH) to C(=O)(NH2)] in a post-pdb2gm scenario? Keep in mind that I have a lot of uniquely parameterised amino acids with unique nomenclature that all visualised packages won't recognise and saving a post-pdb2gmx structure is likely to do something to atom order in the coordinate file (gro or pdb).
I've got just over 100 bond commands in an input file for AMBER tleap. Unfortunately, there is a problem somewhere as I am seeing this output:
/home/ubuntu/miniconda3/envs/AmberTools21/bin/teLeap: Fatal Error!
bond: Argument #1 is type String must be of type: [atom]
usage: bond <atom1> <atom2> [order]
Is there a more friendly error output? i.e., exact WHAT bond command is there a problem with?
Suggestions are most welcome. Please, stick to the topic and to the exact question. Thanks.
I am using amber to run MD simulations and while giving the charge command
charge 1ua7 I obtained the error charge: Argument #1 is type String must be of type: [unit molecule residue. So how to overcome this please help me out. I am attaching the log and pdb file of protein.
I made a covalent docking using GOLD program and obtained the conformations of the ligand bounded with protein.
Now, I want to know a method to calculate the free energy involved in the covalent bond formation between the ligand and protein. Can I obtain this with the AMBER program?
I want to run normal mode calculations in Amber16, but it seems amber is not able to find the necessary program. This is the actual error message:
MMPBSA_Error: Could not find necessary program [mmpbsa_py_nabnmode]
Can anyone help me how to resolve this error?
Can someone please help me with a protocol for parameterizing a metallo-protein for MD simulation with amber forcefield? My protein has two FE molecules and the I tried using either frcmod.ionsjc_tip3p or frcmod.ions234lm_126_spce to generate topology but the system is not minimizing. I confirmed that there are no atomic clashes in my system, so I guess the problem has to do with the ions parameters.
I have the cif file for the unit cell of explosive TKX-50. With the help of VMD software I have prepared the lammps data file with all the necessary information of topology (bond, angle, dihedral, improper). Now I need to input the coefficient parameters for this configuration to prepare the input file for running the simulation in LAMMPS. I intend to use AMBER force field for the simulation.
I have used Amber16 to run a molecular dynamics simulation of my protein system for 50 ns. After the production run was completed, I have generated an MD trajectory with 2500 snapshots which I further analysed using the Cpptraj program. The issue is, after doing a few analyses using cpptraj, the results were generated in the .DAT extension which I can only open in Excel. I analysed the dynamic cross-correlation of all atoms (DCCM), hydrogen bond analysis, Radius of gyration and all the results were generated in the .DAT extension (file format). Therefore, can anyone suggest to me how to change the result file format or what are the software, can be used to view the results generated by AMBER 16? If there is an option in AMBER to visualise this file format, then kindly do let me know as it will help me to progress my research.
I'm simulating a system containing methaneselenol in water and I performed a NPT simulation at QM level using cp2k. Now I want to run a classic dynamics using Amber and using as a starting point the coordinates and velocities of the QM dynamics. How can I convert the files obtained in cp2k and use in Amber?
I believe that in relation to the coordinate I can use the last structure obtained in the .xyz trajectory given by cp2k, but in relation to velocities how could I make this conversion?
Thank you in advance.
How do you all normally analyze multiple MD simulation trajectories. For my system, I ran 5 100 ns simulations using an different initial velocity. Do you perform cluster analysis and then perform RMSD, RMSF etc. from the most popular state or do you analyze each trajectory separately and then average the results?
Is anyone aware of any benchmarks that pit pmemd.cuda (the GPU accelerated AMBER simulation software) against GROMACS' simulation software in a "apples to apples" comparison?
Same protein, water model, salt concentration, temperature, time step, and most importantly, same Hardware configuration.
How to the suites compare in that regard? Are they both 100% efficient and hardware bound? Or does one or the over have an edge in their efficiency and use of hardware to perform the SAME simulation.
Thanks in advance
ps. I've failed to find any 'head-to-head' benchmarks of my own.
I am looking for containers to store samples in the lab, but I didn't find common ground about what type is the best container. Is it plastic? Glass? Amber color? I could think it depends on what analysis I want to store the soil for, but in my case, it is just to keep them in the lab in case I or someone else has to go back to them in the future. I am done with all the analyses but I want to keep 100ml of each soil type.
I appreciate any recommendations or even if you could share with me your providor it would be great. Thank you so much!
I am running MD simulations of a Gold-chelate compound with square planar geometry of Au (III). I parametrized the missing force field parameters for Au and its four neighboring atoms using MCPB and VFFDT properly. The issue is that after the full minimization step (without restraint) in MD simulations, the geometry of Au (III) changes from square planar to tetrahedral which is undesired. Could you please guide me on how to solve the issue?
We need to simulate glucuronic acid (as a part of a larger oligosaccharide) with neutral carboxyl group (COOH) in Amber with Glycam06 forcefield. However, only glucuronate anion is created with Glycam builders and accepted in Amber.
I want to run energy minimization for my protein structure with Amber.
I decided to run more steps of minimization for the whole system compared to the first round of minimization that solute is frozen. I don`t know it`s logical or not.
Do you have any idea about this?
I'm using amber QM/MM, in which QM for a benzene molecule and MM for water molecules. And I can run cpptraj to calculate the dipole of benzene with "vector dB dipole out dB.dat :BEZ"(BEZ is a non-standard residue created by me). But I'm confused when I need to calculate multipole moment like quadrupole moment, because it seems like cpptraj do not support that.
I googled and found that the output file of amber+gaussian contains the information of multipole moment. So do I need to restart my md with amber+gaussian？If must, how to prepare the inputs for the md？And if I could calculate the multipole moment from existing trajectory(which I prefer), how to?
Any advice is appreciated!
I faced a FATAL error while preparing Docked Proteins for MD simulation using Amber20.
But this error does not occur while performing with non-docked protein structures. Is this problem is due to Autodock?
My question is how to add additional DNA/Protein molecules in a simulation unit cell(In Final scenario, a unit cell contains two or more DNA/protein) and how to simulate interaction between them(maybe using peptides)?
I have a rounded piece of Burmese amber (15 mm diameter, 5 mm thick) with 2 alate hymenopterans possibly of the same species (Figs. 1, 2, 3). The tips of their abdomens are very close, and I thought of the possibility of intercourse. The specimens are damaged and many important characters are difficult to explore.
The presence of conspicuous petioles and the general aspect of the mesosoma made me think of alate ants, but I can't be sure! Both gasters have a constriction between the 1st and 2nd gastral segments, and specimen B presents a prora or sternal projection in the 1st gastral segment (Fig. 4). These two characters appear in some species of Gerontoformica.
As said before, the tips of both abdomens are very close. Fig. 5 shows in specimen A two fine spines projecting posteriorly from the gaster and presumably touching the gaster of specimen B.
Specimen A is likely a male. No spines appear in specimen B.
The eyes are large and oval, the ocelli are well detected in specimen A. The labial palps are at least 5-segmented, the maxillary palps are at least 3-segmented. The mandibles are narrow, apparently ending in a single apical tooth. The antennae are long, the pedicel being very short, and the rest of funicular segments longer than the scape and of similar length (Figs. 6, 7), reminding the antenna of Baikurus.
I have generated a model of cellulose bundles using a toolkit named cellulose builder. As an output, it has given (.pdb) and (.psf) files. When I have imported these (.pdb) files into AMBER, it says that some atoms are not in the residue templates.
Could you please give me any suggestion regarding this issue?
How may I import (.pdb) files into xleap of AMBER generated by cellulose builder?
If there is any command, please share it with me.
In the previous questions I have successfully performed and analyzed the MD from two small molecules with Desmond/Maestro. However, I found that MD with Desmond cannot simulate the bond forming and breaking which is a crucial part in the design of our drug delivery system. MD can only gave me the simulation of weak forces.
To the best of limited my knowledge, I found two ways. 1. Reaxff reactive force field. 2. Quantum mechanics simulation (QM/MM).
I tried the Qsite (a tool of QM/MM in the maestro), but it did not gave out a trajectory file that can be visualized and analyze with MDanalysis. So, I turned to Reaxff. Now, I am trying to use Amber/Reaxff package to do the simulation. Right now, I faced some installation errors in Amber. I have sent the problem to the Amber mail list.
My main goal is to simulate the reaction between two molecules (the binding of the drug delivery agent and the target ligand) Both of them are small organic molecules.
My questions are:
1. How can I analyze and visualize the results (trajectory) from QM/MM?
2. After the simulation from the Amber/Reaxff, how can I analyze and visualize the results (trajectory)? I found some information stating that traditional MD viewer and analyzing tools cannot do the job. Can you suggest some software that I can dive into?
3. How to get the parameterization of the small organic molecules?
Is my approaches correct? Please, I really need your advices.
Thank you very much for your help!
Dear RG members,
I am trying to install AMBER in parallel in one cluster having ifort compiler. I am getting the error MPIF90 command not found. I read the configure2 file in AmberTools/src, that tells I need to install serial first.
setenv AMBERHOME "amber path"
./configure -noX11 intel
It is running perfectly.
How can I proceed to add MPI run.
Kindly suggest the next commands.
Should I hit
./configure -mpi intel
or some other tricks.
I am failing each time with few errors.
Kindly share the complete commands after the searius installation steps.
After docking of a small ligand to a protein, I am interested in simulating the protein-ligand complex in amber. However, I donot know how to use the information in the dlg file. Any help in this regard would be highly appreciated.
I have several sets of MD runs and I would like to perform PCA analysis using Amber.
I am quite a newbie with this package being mostly used to Gromacs/NAMD.
In particular I would need to calculate:
1- The histogram of the first 5 eigenvalues
2- Dot product of the essential deformation modes taking into consideration the first 10 eigenvalues (which should describe the ~90% of the driving motion).
Do you know which chain of commands put together to achieve the goal?
Thanks in advance to anyone for you kind help.
The main point is that I would like to perform the molecular dyanamics of two organic small molecules, more specifically, two PEG-polymer with two molecules one on each that could potentially interact with each other. I would like to use MD to find out the interaction between two molecules when they installed on PEG polymer.
I summarized the question at the first:
1. What is the best way to perform the MD with two polymers or two small molecules (I tried with small size at first).
2. How could I analyze it (RMSD, RMSF with both molecules to its original state, paired RMSD, MMPBSA, contact surface and radius of gyration and etc.)?
3. Is there any references or tutorial that can guide me?
The following part is the methods that I tried:
First, I tried with Gromacs. But the parameterization of non-standard residues of small molecules is painful and not accurate with the server out there... The combination of two molecules into one topology file is also painful. So, I transfer to Desmond. Recently, I got my small molecules simulated with Desmond. I would like to analyze the trajectory file with RMSD, RMSF with both molecules to its original state, paired RMSD, MMPBSA, contact surface and radius of gyration. But, with the interaction diagram of Desmond, it cannot allow me to use two small molecules. It force me to use one protein and one ligand... I want to analyze the interaction of two small molecules instead. Or is there any some tricks to make it work?
Therefore, I tried with mdtraj, a python based MD analysis library.
The out.cms file (topology from desmond) cannot be recognized by the mdtraj...
So, I tried to convert the .cms to mol2 with VMD. But, it turned out the column of the atom coordinates is 9 instead of 7 that is recognizable by the mdtraj.
I created a script to remove the additional column. However, another error was raised
I got stuck here... How could I analyze the trajectory of two small molecules?
Should I re-run the MD with other program such as Amber or Gromacs?
Currently, I am setting up AmberTools21 and try to use Antechamber to parameterize the molecules and try to perform the MD and analysis with AmberTools. But, I don't know if it will work...
Please give me some advice, guide and suggestions. Thank you so much!
I'm really looking for your guidance and help in order for me to pursue my next step in computational work. I'm new to computational work and keen to learn more. Currently, I'm using AMBER 16 to do Molecular Dynamic (MD) simulation and trajectory analysis. The protein I'm working with is 5IBE. I used CPPTRAJ to extract RMSD'd PDB's from trajectories. I extract specific frames of the trajectory in a 2drms plot, to generate the average structure in PDB format. This is the script I used to generate the average PDB structure from a 2drms plot.
trajin 5IBE_heme_md_pc.binpos 2100 2500
rms first mass @C,CA,N
average 5IBE_heme_md_pc_2100-2500.pdb pdb
2100-2500 is the frame value from the 2drms plot. I have attached my 2drms plot for your reference.
My question is do I need to minimize the average PDB structure that I got from CPPTRAJ analysis before continuing with molecular docking? Is that ok If I continue using this average PDB structure for the docking process without minimization? Please let me know, I need some clarification.
I would be grateful for every suggestion that will be given to me.
Thanks & Regards
Hi, i'm trying to execute a QM/MM simulation by ONIOM scheme using GFN2-XTB/Amber interface on Gaussian 16, but gave an error to do the frequency calculation.
Another problem is to execute GROMACS/ORCA interface using XTB, because ORCA doesn't compute analytical frequency.
I have a computer with one CPU (Intel Xeon Gold 6134 Octa-Core 3.20 GHz Processor) and GPU (Nvidia RTX 2070).
I want to perform temperature replica exchange Molecular Dynamics on this machine, so I installed Gromacs. However, I found that it needs MPI and multiple CPUs more than the number of replicas.
I found Amber and NAMD treat GPU better than Gromacs, but I cannot figure out whether they can run REMD on a single CPU because in their manual they use MPI as an example.
I've run a simulation for an apoprotein using fourierspacing = 0.16, and I want to run a protein-ligand complex simulation (all using Amber ff). I found that it's suggested to set the value of fourierspacing to 0.125, if I did so, will it affect the results of the simulation much when I reach the point of comparing the apoprotein and the protein-ligand complex simulation? or should I keep it to 0.16?
Hi. I'm learning molecular dynamics simulation, where I came across different types of forcefields like CHARMM, AMBER, GROMOS, OPLS . What are few differences between them ?
I found a really interesting Burmense amber that I want to buy. However, the seller doesn't know exactly in which mine or date it was collected. Once it was traded several times.
I know how to test if it is copal, real amber, or artificial resin.
However, is there a way to confirm if that amber is really Burmense from Cretaceous and not Eocenic Baltic amber? Is there an institution that can certificate it for me for an affordable price?
I would like to perform steered Molecular Dynamics (sMD) to investigate conformational changes of the protein from the initial to the final form. I've got both initial and final coordinates of the protein in a form of PDB, I'd like to conduct simulation for 100-200ns and extract intermediate structures.
Has anyone performed such study using AMBER suite and can supply any how-to?
I am using Gaussian's ONIOM software for this calculation. And receive the following error message :
Missing atomic parameters for atom 234 IAtTyp= 0
Missing atomic parameters.
I have tried to use the parmlookup function in addition to trying multiple keyword combinations but I cannot seem to get past this error. Atom 234 in this case is a carbonyl carbon that links the QM region to the MM region of my calculation
My job input is as follows:
#p oniom(B3LYP/6-311G(d,p):amber=hardfirst) nosymm scrf=(smd,solvent=water,oniompcm=x) geom=connectivity iop(2/15=3) test opt=quadmac
I've also tried the following keywords are replacements:
This error occurs after 12 PCMM matrix inversion algorithm cycles and the MM parameters for the model system are supposedly made.
I have attached my .com and .log files for the job
I performed a 100ns run for several drug candidates, and i wanted to check their average binding energy using g_mmpbsa. the thing is that g_mmpbsa gave me a very high positive energy for a my reference compound which is a known inhibitor as follows:
#Complex Number: 1
van der Waal energy = -225.720 +/- 13.278 kJ/mol
Electrostattic energy = 3866.697 +/- 82.399 kJ/mol
Polar solvation energy = -637.863 +/- 87.628 kJ/mol
SASA energy = -18.475 +/- 0.895 kJ/mol
SAV energy = 0.000 +/- 0.000 kJ/mol
WCA energy = 0.000 +/- 0.000 kJ/mol
Binding energy = 2984.639 +/- 65.708 kJ/mol
I noticed the problem to be in the electrostatic energy term. after some research I came to know that to overcome such overestimation for highly charged systems. I should use a higher dielectric constant. so these results was at dielectric constant of 2. So, I went for 4,8, and 16 on a shorter range of the trajectory. the electrostatic term kept decreasing and the binding energy as well but stayed positive for constant at 4, and 8. for constant at 16, it gave me binding energy with a negative value ~ - 250. but when using constant 16 with another less stable candidate it gave me ~ - 350. So, I concluded that the electrostatic term is still overestimated so that it affects the relative values between the candidates. here, I went for a very high dielectric constant of 50 to drastically decrease the effect of the electrostatic term. So, at constant 50, the reference compound gave a binding energy of ~ -710, while the less stable molecule gave ~ - 650.
this is the output for the reference compound at constant 50 :
#Complex Number: 1
van der Waal energy = -226.401 +/- 9.161 kJ/mol
Electrostattic energy = 154.710 +/- 2.537 kJ/mol
Polar solvation energy = -620.464 +/- 21.843 kJ/mol
SASA energy = -18.605 +/- 0.766 kJ/mol
SAV energy = 0.000 +/- 0.000 kJ/mol
WCA energy = 0.000 +/- 0.000 kJ/mol
Binding energy = -710.760 +/- 23.953 kJ/mol
so now it gave a right relationship between the two molecules. the question is there something wrong with what I did? is it reliable to go for such high dielectric constant =50? is there a better way to fix this ?
thanks in advance
I'm using Gromacs 2020 to run a protein ligand simulation using Amber99SB for protein and Amber (GAFF) for ligand, in the mdp files should rlist be of the same number as rcoulomb and rvdw e.g. in case of Amber ff , should it too be set to =1.0?
I've read that the cutoffs are specific for each force filed, and that in Amber FF it's about 1.0, and in CHARMM about 1.2, am I getting it right? And if anyone can provide me with a reference for those cutoff values and parameters used in mdp files other than the gromacs manual itself, I'd be grateful.
Thanks in advance
I am performing my simulations on Amber 16 and there is a lot of confusion in the tutorials.
First, we should prepare topology files for ligand and protein separately and then combine them to make a complex. right?
Second, when we do the energy minimization step we do the minimization of the whole system but in scripts complex name or any file isn't mentioned?
Third, what is the purpose of preparing gas.prm7, and wet prm7? which is more important.
and when I searched for preparation of MD script it was so confusing with long paths. is there any tutorial or online software where we can paste our files and received the md.csh file?
if anyone knows kindly respond.