- Berke Piskin added an answer:How can I understand the atoms placement in a layered structure?
I would like to understand the structure of my sample. I know my sample, however I am not sure about where atoms take place. They could be separated layer by layer or they can be sited on the same layer all together. I searched, asked and tried some methods. The last one that I learnt and haven't tried yet is that using EXPO which is followed by SIRPOW. And I've tried EXPO only during 2 days seminar and never used SIRPOW. In the second way GSASII has ability to do it, am I right? Is there anyone who have tried before and can advice me? Thank you!
Perfect, thank you very much. Nowadays, I also try to understand GSAS II. And also FOX will be the other one. Thank you for your help. I hope I will find a solution. Best regards.Following
- Karsten Krogh-Jespersen added an answer:Why am I getting a convergence failure in my qst2 calculation using reactant and product structures?
The order of atoms in the reactant and the product are exactly the same, I had used DFT , B3LYP, 6-31g(d) for doing that
Do your best and throw in your 'best guess' for the TS, and change the keyword to qst3. I have never had qst2 converge on anything; my success rate with qst3 is only slightly higher. Bartosz' suggestion is a good one, in particular if you are dealing with transition metal complexes, where optimized reactant and product geometries may differ widely.Following
- Ahmad Mani-Varnosfaderani added an answer:Any inputs for a list of Drugs (market/clinical trials) designed/discovered using Computer Aided Drug Designing?
I was collecting information about the list of drugs designed/discovered using Computational Chemistry. Any inputs?
For downloading the clinical drugs you can go thorough the DrugBank webpage.
The link is as follows:
Here, you can see different sets of drug molecules, classified as:
Approved Drugs, Experimental Drugs, Nutraceutical Drugs, Illicit Drugs and Withdrawn Drugs.
The downloaded molecules are in SDF format and can be opened via different molecular display softwares such as MolView or Discovery Studio.
I hope it helped.
Assistant Professor of Computer-Aided Molecular Design,Following
- Danish Jasnaik added an answer:How can a TarFisDock file submission problem in Reverse docking be solved?
I have a problem in submitting my Mol2 file to TarFisDock. After browsing, selecting my file and choosing the target proteins, when I clicked submit, I got the following reply:
“You have submitted a valid Mol2 file!FTP connection has failed!”
After keeping trying to submit it, I got the following reply:
“You have submitted a valid Mol2 file!You have already submitted 5 jobs today, please submit new jobs the other day!”. Although, I have not received any job ID to my e-mail.
Please, how can I solve this problem?
It is worth to be noted that TarFisDock forum is useless, how can one get support for using it.
It may be possible that you get this error due to internet connection problem or may be their server is overloaded, you can also check your spam folder in your mail, or can try resubmitting it again. Hope this helps.
- Lucas Fagundes Esteves added an answer:Has anybody had problems with IRC calculations within a PCM model?
I am investigating the hydrolysis process of phosphate esters using PCM model to simulate the surroundings of the reactive system. The process is completely described in gas phase, however in aqueous phase I have had some problems with the Intrinsic Coordinate Reaction (IRC) analysis. The behaviour of the curve was not normal and two main problems were observed:
1 – When I try to obtain the IRC in two outputs, by specifying the forward and reverse keywords in the calculation line, what I get is the same path, i.e., the reactants reach the transition state (in the forward calculation) and after that the transition state reach the reactants once again (in the reverse calculation).
2 – After this problem I tried to change the IRC parameters and I put a different stepsize and a diferent maxpoints. In this situation the change of step size were not regular and in one extremity of the curve the IRC points accumulate in the same region, where the stepsize remained practically unchanged.
The set of keywords were:
# irc=(calcfc,maxpoints=60,forward,stepsize=20,maxcyc=200) scf=(maxcycle=200) b3lyp/gen gfinput pseudo=read scrf=(pcm,read)
At the end of input:
Has anybody here had a similar problem in IRC calculations using the continuum approach?
I really appreciate any help you can provide.
Dear Mihai, thank you for your suggestions. I spend the weekend analizing my structures and your intuition was right, the IRC for normal mechanism is wrong. The TS is right but the IRC was conducted assuming the gas phase as the surroundings, and the TS strucutre was obtained within the continuum media. So I remake the calculations using now the IRC in aqueous phase:
# irc=(calcfc,maxpoints=60,forward,stepsize=20,maxcyc=200) scf=(maxcycle=200) b3lyp/gen gfinput pseudo=read scrf=(pcm,read)
The problems with points accumulating in the extremity of the curve has appeared again, but the calculation is still running. I will wait until it finishes to comment about the results.
Once again thanks for the helpful assistance
Dear Prerna, unfortunately i did not find any solution until now, but I am working hard to understanding what is happening with IRC calculations using PCM. I saw a comment in Joaquim Barroso's Blog about an incompatibility between IRC and PCM in Gaussian 03 (though I'm using G09), but he says that it is not true for Gaussian 09, where there is a new algorithm for PCM calculations.
I am looking for similar problems in CCL, but I did not find anything similar until now.Following
- Bojidarka B. Ivanova added an answer:Can anyone please provide me any reference for non bonding forcefield parameter for iodate anion???
(IO3)- non bonding parameter for molecular dynamics simulation...
Please find below three refs about the quantum chemistry of your ion, but the first screening has shown that there have not data for the potential energies. may be somewhere in the cited reference would have...
1. Ab initio calculations for some oxo-anions of chlorine, bromine and iodine, Christoph Oberle, Hans H. Eysel, Journal of Molecular Structure: THEOCHEM, Volume 280, Issue 1, 11 March 1993, Pages 107–115
2. The Journal of Chemical Physics, Volume 70, Issue 9, 1979, Pages 4194-4198, Vibrations and force constants of the hexagonal lithium iodate crystal, Crettez, J., Misset, J., Coquet, E.
3. The electronic structure of ClO−3, BrO−3 and IO−3: an SCF—Xα study, B.El-Issa, A. Hinchliffe, Journal of Molecular Structure, Volume 67, 1980, Pages 317–321Following
- Mai H. El-Naggar added an answer:What's the best way to proceed for reverse docking - Target fishing?I have a small endogenous molecule whose effects are partially known but its mediators are not. I'd like to try a reverse docking approach to investigate this mediators, screening the molecule against various libraries of known receptors. What's the best way to proceed? Any suggestions?
Both TarFisDock and PharmMapper need Mol2 file. I read in TarFisDock forum that it can be obtained as follow:
3 steps are needed to get a MOL2 file.
1. Get 2D sketch
2-D structure of small molecule can either be sketched using ISIS/Draw or ChemDraw.
2. Get 3D coordinates
3-D coordinates of small molecule were obtained using
VEGA Online MolEdit
http://nova.colombo58.unimi.it/moledit.htm(This service provides partial charge together with 3D structure)
3. Assign charges
In SYBYL or InsightII and added Gasteiger charge, then saved in mol2 format for TarFisDock docking.
Or using some free software such as Open Babel to calculate Gasteiger partial charge.
I think using Chimera or Open Babel are the best choices.Following
- Rafał Szabla added an answer:Quantum Espresso users! Do you know how to enforce triplet multiplicity in a PWscf calculation?
I'm a beginning QE user. I would like to perform a calculation of TiO2 surface with O-vacancy. Since two of the surface Ti's will most likely have 3+ charge, there will be two unpaired electrons in the system. Unfortunately the QE manual is very unclear about it, and one needs to set several keywords like "nspin" and "starting magnetization". I want to actually check in the beginning if the closed shell and spin polarized calculations converge to the same of different minima, to be sure what to do in further steps. Do you have any ideas for a proper set of settings in the input file? What about the DFT+U correction?
Thanks in advance for help!
Hi Sergei! Now everything is clear. Thank you very much for your patience and for the detailed explanation!
- Tikaram Neupane added an answer:Can any one help me with a Quantum Espresso Error?
I am trying to run Quantum Espresso software. But it says " /home/tikaram/espresso-5.0.2/PW/examples/example01 : starting
This example shows how to use pw.x to calculate the total energy and the band structure of four simple systems: Si, Al, Cu, Ni.
executables directory: /home/tikaram/espresso-5.0.2/bin pseudo directory: /home/tikaram/espresso-5.0.2/pseudo temporary directory: /home/tikaram/tmp checking that needed directories and files exist...
ERROR: /home/tikaram/espresso-5.0.2/bin not existent or not a directory Aborting
- Najme Dehghan added an answer:How can I set the pressure in NPT phase of molecular dynamic simulation?
We could set temperature with kinetic energy in MD. How about pressure in NPT phase?
thanks for your useful suggestions.Following
- Danish Jasnaik added an answer:Is the aminoacid sequence of PDE-1 type 5 venom of Bothrops atrox available?
I am unable to find amino acids sequence of PDE-1 type 5 venom of bothrops atrox in any sequence database. I am interested to target this protein for computational studies. Kindly guide me, if sequence of this target is available?
Yea i know that. One thing you can do is take this sequence an BLAST it to find out your desired sequence it might help you to get it.Following
- Justin Lemkul added an answer:How long does it take for amyloid peptides to form random coil structures ?
I am doing MD simulations of Amyloid 1-42 monomer using gromacs,at three different velocities, my simulations has completed around 500ns each, but still peptide is in helical form. I have read Justins papers, in his simulations in only 150ns structure showing random coil structure ? Can anyone help me in this ?
There are a number of other AMBER parameter sets that could have been used. There's a rabbit hole one can descend easily :) We mostly wanted to compare force fields that had different parametrization methods, though obviously it's a living issue, one that every investigator needs to consider. Hopefully our work is simply an illustrative example of the larger point.
If anyone needs a reprint, just email me.Following
- Ferhati Azedine asked a question:Is there any one experienced with Polyrate2010 to give me a file.dat as example with the option status 6 for all species involde in a reaction path?
We have just installed on our HP z820 station the soft of truhlar polyrate 2010 and need to begin with a simple usefull example with the status 6 in the .dat file , any help is kindly welcomeFollowing
- Robert J Paruch added an answer:How do you output the trajectory file in MD simulation?
Sorry about the confusing title.
I am talking about the output frequency to write the trajectory file. Normally, the time-step in MD simulation is 1 or 2fs. And I am using 1ps/frame to output the trajectory file. The file size is big. And when I analysis these files. I choose 10ps/frame. I found it's hard to find difference to analyze the file between 1ps/frame and 10ps/frame. So should I change the frequency to write the trajectory file to 10ps/frame to save space?
How often do you guys store the trajectory files?
One can also think of a variable output frequency if this is appropriate for the system and kind of simulation. For example, output frequency has to be high during the high energy stage of the simulated proces, when particles move quickly. Then, as the system equilibrates, the output frequency can be reduced. It helps to decrees the size of the output file, keeping the relevant information.Following
- Grant Hill added an answer:Computational chemistry: How to handle basis sets for heavy atoms when using CBS-QB3?
I'm treating species which have C,B,H,X=F,Cl,Br with CBS-QB3, but entering heavy atoms such as I, Sn, and Pb, an extrabasis of lanl2dz gives a 502 error "Inaccurate quadrature in CalDSu" and I don't know what this is. I've also tried STO-3G, and 3-21g for these heavy atoms (as extrabasis), but the result is the same. otherwise, a 301 error with a message of
Standard basis: 6-311G(2d,d,p) (5D, 7F)
Atomic number out of range for 6-311G basis
what should I write to come up with these errors and optimize the compounds?
As others have mentioned, CBS-QB3 (and the other composite CBS methods in Gaussian) is a completely 'automated and prescribed' method. If you look at the Gaussian manual page for the method (http://gaussian.com/g_tech/g_ur/k_cbs.htm) you will see the following text:
"No basis set should be specified with any of these keywords."
Indeed, if you read the original papers for the method you'll see it makes no sense to define a basis set - several different basis sets are required (for each element) to carry out CBS-QB3. If you want to include an element that is not defined in the method then I am afraid you are simply out of luck.Following
- Sayyed Faramarz Tayyari added an answer:How to properly apply Gaussian G2 method?I would like to ask what is the proper way to use this Gaussian composite method for high-accurate energy calculations? Do I need to pre-optimize my molecule using the same functional and basis set (in this case: MP2/6-31G*) as its required for starting geometry in G2 method? Or maybe this pre-optimization step is done automatically within G2 method and there is no difference what functional/basis set was used to prepare initial structure? Moreover, should I use OPT keyword or just G2 alone? I noticed that in case of correcting energies of transition state structures, the OPT(TS) keyword was needed, otherwise the molecule was optimized either to reactants or products.
Simply type G2 or G3 then everything goes automatically. However, you cal also apply
solvent effects by adding, for example, SCRF=(PCM,solvent=...).Following
- BASANT ALI HASSAN WALI-ELDEEN ALI added an answer:How Can I draw a crystal structure to be used for G09?
I want to draw a crystal structure for Perovskite lead crystal and to optimize it using G09 , I searched for the cif file but all cif files were not in the same configuration I want
So I want to draw it myself , I Tried Vesta but it didn't help
Thanks very much this is very goodFollowing
- taki eddine ahmed Ardjani added an answer:How Can I calculate potential energy distribution PED% with VEDA?
Does somebody know how to calculate PED%, I'd be very grateful if anybody could give me Further information about procedure to calculate PED% with veda programme.
I really appreciate any help you can provide
- M. K. Awad added an answer:How can I do encapsulation of organic compounds at the cavity of Beta-cyclodextrin?
This question is with regards to computational chemistry.
Thanks a lot and appreciated. It was really helpful.Following
- Sai Siddhardha R. S. added an answer:How can I do proton adsorption studies on Metal nanoparticles in Materials Studio software?
Can you please give me the details of the parameters involved in it....
Thanks Saeed Kazemiabnavi, I'm studying electrochemical reduction of proton by applying a cathodic reduction potential.(Hydrogen eveolution reaction)
I would like to study the proton adsorption energy on different nano particle surface computationally, before going on to do a real experiment.
This helps me to nail down the right system for the reaction.
Can you please suggest me in this regard on how to screen the materials for Hydrogen evolution reaction using Materials studio Software.
What kinda parameters involved in it?Following
- Vijay Manickam Achari added an answer:We do my DFT calculations on sugar+lipid systems give CPHF error?
I am doing DFT calculation on sugar lipid system. The command I used is
"#n opt freq=noraman b3lyp/6-311++g(d,p) geom=connectivity scf=qc".
I get error message as below:
LinEq1: Iter=992 NonCon= 1 RMS=2.17D-10 Max=3.09D-09 NDo= 1
LinEq1: Iter=993 NonCon= 1 RMS=2.14D-10 Max=3.02D-09 NDo= 1
LinEq1: Iter=994 NonCon= 1 RMS=2.23D-10 Max=2.91D-09 NDo= 1
LinEq1: Iter=995 NonCon= 1 RMS=2.05D-10 Max=2.41D-09 NDo= 1
LinEq1: Iter=996 NonCon= 1 RMS=2.03D-10 Max=2.61D-09 NDo= 1
LinEq1: Iter=997 NonCon= 1 RMS=2.10D-10 Max=2.61D-09 NDo= 1
LinEq1: Iter=998 NonCon= 1 RMS=2.24D-10 Max=2.65D-09 NDo= 1
LinEq1: Iter=999 NonCon= 1 RMS=2.08D-10 Max=2.47D-09 NDo= 1
LinEq1: Iter=*** NonCon= 1 RMS=2.07D-10 Max=2.51D-09 NDo= 1
CPHF failed to converge in LinEq1.
Error termination via Lnk1e in /pkg/chem/gaussian/g09d01/g09/l508.exe at Mon Jan 5 17:54:15 2015.
Job cpu time: 10 days 13 hours 0 minutes 32.4 seconds.
File lengths (MBytes): RWF= 6033 Int= 0 D2E= 0 Chk= 98 Scr= 1
Error: segmentation violation
rax 0000000000000000, rbx ffffffffffffffff, rcx ffffffffffffffff
rdx 000000000000abd9, rsp 00007fffac218c08, rbp 00007fffac2191f0
rsi 000000000000000b, rdi 000000000000abd9, r8 0000000000000000
r9 00002afe95f83e10, r10 ffffffffffffffff, r11 0000000000000202
r12 0000000000000000, r13 0000000000000000, r14 00007fffac219238
--- traceback not available
Can anyone give a suggestion on how to eradicate this error?
Thanks in advance.
Dear friends, many thanks for your suggestions. As for now I have tried B3LYP/6311g(d), and the calculations are running fine. My systems contain shorter alkyl chain and longer chain which are varying from 8 to 24 carbons each chain. The 6311++g(d) only give problem for higher number of chains like above 12 () may be due to higher number of atoms. As for next step, I may try suggestion by #Filippo, for the longer chains to see if they could converge.Following
- Vernon G.S. Box added an answer:While constructing a hydrogen bond table from .lis file( platon) how can I judge which interactions within a crystal are most appropriate to consider?
We generally construct hydrogen bond tables seeing the .lis file generated from platon. However,out of all interactions within the crystal, it is necessary to include all of it in the hydrogen bond table? If not, how do we judge which interactions are really appropriate to include? What if two interactions are competing and mutually exclusive? Which do we leave out? Is it really that we should look at the 'survival of the strongest' hydrogen bond all the time?
The inability to automatically construct a valid and thorough connectivity table from coordinate data only is one of the major failings of most molecular modeling programs.
StruMM3D does this, automatically, and the connectivity table will include ALL hydrogen bonds present/possible.Following
- Sergio Galembeck added an answer:Is DFT a better method than CCSD(T)/cbs?
Recently I recalculate the thermochemistry of a reaction with CCSD(T)/CBS and the results are more lower in energy than how I assumed. The original information was with B3LYP/6-311++G(2d,2p).
My question is: Can I consider my data better? CBS basis set, it isn't very difficult (for small systems) but it didn't seem to be very applied in general., have some consideration or problem that I should know about this extrapolation?
Thank you for your time
Don't forget to take a look on D1 or T1 criteria given by CCSD(T) calculations. There are some systems that are not well represented by a single configuration. In these cases you need to do some tests using CASSCF.Following
- Kyle E. Hart added an answer:Can bond be formed during simulation in Lammps?
I am working with crosslinking of polymers. during simulation wanted to make bond. is it possible to do in lammps? how to account for the forcefield parameter for the newly formed bonds during simulation.
We created an open coursed simulation package that is able to form bonds in LAMMPS (and subsequently polymers).
See paper: http://link.springer.com/article/10.1007/s00214-013-1334-z
Link to software in paper. Try it out!Following
- Mckay Easton added an answer:G09 output Frequency Calculated twice Why?
In g09 Opt+Freq calculation i used the following comment in Route section
#P M062X/6-31G* Opt=(gdiis, CalcAll) scf=qc Freq TThe job was done fine but I found the frequency is calculated two times in the output. Can anybody please explain why it calculated two times
When you use the opt=CalcAll keyword, the frequency is automatically calculated, since it has already gone through the effort of calculating the Hessian for the final optimization step. Then you added the Freq keyword, so it calculated it a second time.
From G09 website:
Specifies that the force constants are to be computed at every point using the current method (available for the HF, MP2, CASSCF, DFT, CIS, and semi-empirical methods only). Note that vibrational frequency analysis is automatically done at the converged structure and the results of the calculation are archived as a frequency job.Following
- Closed account added an answer:Can any one help in the parameterization of ZN metal using MCPB?
I want parameterise the ZN metal, which is coordinated with CCCH (three CYS and one HIS residues) residues. I just followed MCPB tutorial. While side chain modelling i got errors and unable to fix the problem. Here, i have attached my pdb file , sidechain.bcl file and sidechain.bcl log files.
ANDDEAR RESEARCHER,I AM THE FIRST ONE TO ANSWER,HERE IS MY COMMENTS, the Protein Data Bank (PDB) contains over 18,000 structures that contain a metal ion including Na, Mg, K, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Pd, Ag, Cd, Ir, Pt, Au, and Hg. In general, carrying out classical molecular dynamics (MD) simulations of metalloproteins is a convoluted and time consuming process. Herein, we describe MCPB (Metal Center Parameter Builder), which allows one, to conveniently and rapidly incorporate metal ions using the bonded plus electrostatics model (Hoops et al., J. Am. Chem. Soc. 1991, 113, 8262-8270) into the AMBER Force Field (FF). MCPB was used to develop a Zinc FF, ZAFF, which is compatible with the existing AMBER FFs. The PDB was mined for all Zn containing structures with most being tetrahedrally bound. The most abundant primary shell ligand combinations were extracted and FFs were created. These include Zn bound to CCCC, CCCH, CCHH, CHHH, HHHH, HHHO, HHOO, HOOO, HHHD, and HHDD (O = water and the remaining are 1 letter amino acid codes). Bond and angle force constants and RESP charges were obtained from B3LYP/6-31G* calculations of model structures from the various primary shell combinations. MCPB and ZAFF can be used to create FFs for MD simulations of metalloproteins to study enzyme catalysis, drug design and metalloprotein crystal refinement.
PMID: 20856692 [PubMed] PMCID: PMC2941202 Free PMC Article
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- Denis Mulliner added an answer:Is it possible to do canonical forms studies using gaussian?
Is it possible to do canonical forms studies using gaussian?
I am not entirely sure what you mean by canonical forms studies but it seems very unlikely that they are possible with gaussian. Several canonical forms or resonance structures are a way to depict the same delocalized state using localized representations in written form. They are used if the state of the molecule can't be represented by a single Lewis formula. Quantum mechanically they don't exist. Any SCF method, if Gaussian or Gamess or Mopac or any other software, will produce the delocalized state.
It might be possible to study different resonance structures using a force field approach. But I am no expert on that and it still sounds not very useful.
If you could explain why you would do these studies it would be easier to find a solution to your problem.Following
- Sayyed Jalil Mahdizadeh added an answer:What is the best software (open source or free) for molecular structure optimization?
I am going to developing models for prediction of melting point of some hydrocarbons component with QSPR method. i have one sdf file which contain those hydrocarbons structure so before calculating descriptors the structures should be optimized. i need a software which as an input get my sdf file and optimize the whole structures file. Also i was wondering is there any difference between descriptors which calculated base on optimize structure and not optimize one.
I think you have to use MD simulation with large number of atoms with PBC to get a reliable and precise melting point. So you dont need a high level qunatum mechanics optimization on this matter. As you mentioned a light pre-optimization using semi-empirical methods (like PM6, PM3, or AM1) is nice to do. I recommend the gaussian 09 program package of course is not free. Also you can use the Hyperchem which also is not free. If you really need a free software, then Orca is a good choice. After a pre-optimization you can use LAMMPS MD simulation code (free :)) with a large simulation box with PBC and an accurate force field (i suggest AIREBO, Tersoff or Reactive force fields all are implemented in LAMMPS). You can use a thermostat to increase temperature gradually with time. Finally, monitoring some properties like density, RDF and MSD lead you to the melting point.
- Ferhati Azedine added an answer:Usually, 2070 Error of Gaussian03 in Windows is caused by computation capacity deficiency. Other causes in relation with this error (IRC and TS calc)?
Actually I try perfom calculation of TS and IRC for a E/Z isomerization of a system of Natoms=27
some times it's caused by an error in the input file check first the key words in the
- Cody Covington added an answer:How to add improper torsion in simulated annealing?
I am doing simulated annealing on a few guanine molecules, but when I see the generated structure after simulation, each molecule is planar, but they are all non planar related to each other. I know they should be planar because QM calculations show them as planar. I was wondering if I should add any keyword in order to keep them planar?
Sorry i am unfamiliar with the term 'referent'. Does that mean that they are neighboring Guanosines on a chain? Could you include a picture? with frcmod files, I assume you are using amber?
Also I think it will be complicated because the guanines are probably in different molecular groups. The topology file builder (tleap in Amber) may not correctly add the improper dihedral, and you may have to edit the topology directly (which is a pain).Following