How to carry MD simulations with distance constraint between two residues?

Dear all

I am simulating a protein-ligand complex. During the course of simulation, the cofactor moves far away from the substrate. I want to add distance restraints between protein backbone and cofactor atoms. I refer the manual and tutorials but did not get the full understanding of how to put distance restraint. Could you please help me to do this? Regards Sadaf

Hello, all.

I am planning to run MD simulations of membrane-protein system with Amber program.

Then, I would like to know how I work different position restraints which are assigned in separated groups like membrane, flexible parts of a protein , rigid parts of a protein and so on in some steps of equilibration.

In Gromacs, you can assign position restraints differently with index file. Is there any way in Amber like the one in Gromacs?

Actually, I have used Gromacs for a long time, and I have started using Amber recently for some reasons, but I have little knowledge about schemes in Amber...

I would be really happy if I got any helps.

Thank you, in advance.

I want to perform a protein-ligand MD simulation using Amber. I have generated ligand frcmod, lib, rst7, and prmtop files. Then, I loaded my complex file, which contained the ligand and protein in water (generated using Packmol-memgen). However, when I tried to save the rst7 and prmtop files for the complex, I encountered this error: 'FATAL: Atom .R<***> does not have a type.' I've attempted to resolve this issue multiple times, but it keeps happening. I followed the tutorial exactly as outlined on the AmberMD website ('Simulating a pharmaceutical compound using Antechamber and the Generalized Amber Force Field'). Surprisingly, the problem persists. even though I tried to use the same molecule, protein, and files provided on the website to check out if there were any problem with my own files and again i ended up with same problem. Can anyone help me figure this out?"

I created .prmtop topology and .inpcrd coordinate files in tleap, and then I ran minimization, heating, and equilibration steps, and then 10 ns of production with pmemd in AMBER 14 and created .rst and .mdcrd files for my protein-ligand complexes, I noticed when trying to view the trajectory in VMD, it looked like my complex went out of the box during some steps, and I just want to make sure I'm looking at the files correctly since I'm new to MD simulations. In VMD, I used the command "vmd complex.pdb", and then loaded the complex.prmtop file and then the complex.inpcrd file, and then the min.rst, heat.rst, and equil.rst files, and then the production.rst files for each of the 10 nanoseconds. Is this the correct way to view trajectories in VMD? What is the purpose of visualizing the trajectory for MD simulations?

When trying to load the files for one of my complexes in VMD, I noticed that my complex.inpcrd, min.rst, and equil.rst files jumped around on the screen into different positions, but after the prod.rst files, it stayed relatively in place. I also noticed that for some of my complexes, the RMSD didn't converge completely after 10 ns because there were very sharp sudden peaks in my RMSD graphs that I created with cpptraj, so I was wondering if the issue could just be my settings during the MD simulations, or if I'm selecting the wrong files to load into VMD. Should I load the .mdcrd files instead of .rst, or would there not be a difference?

In computational chemistry there is point where we have to put the multiplicity value as singlet, triplet etc.

I want two fix a part of protein(trans-membrane protein) using distance restraint so that when we apply force on upper half of protein, this fixed portion also moves automatically and no separate force is required to move it.

I am using PDB file 5F9R of CRISPR/Cas9 pre-catalytic state structure for molecular dynamics simulation with AMBER. It is a complex of protein, DNA and RNA

First I ran the command:

pdb4amber -i 5f9r.pdb -o 5f9r_new.pdb --reduce --dry

then I used the following script to solvate the protein and add counter ions.

source leaprc.protein.ff14SB source leaprc.water.tip3p loadamberparams frcmod.ionsjc_tip3p crispr = loadpdb 5f9r_new.pdb solvatebox crispr TIP3PBOX 12.0 charge crispr addions2 crispr Cl- 0 saveamberparm crispr crispr.prmtop crispr.inpcrd quit But at the last step, the parameters cannot be saved because of this kind of errors:

FATAL:  Atom .R<DG 1535>.A<C4 22> does not have a type.

It seems that the certain names of atoms in PDB file cannot be recognized by LEAP. I think this is caused by the atoms on DNA chain in the structure. (DG, DA, DT, DC are names of basic groups in DNA)

How can this problem be solved?

Thank you for your help.