shyamala iyer wrote:
Hi gromacs users,
I apologize in advance for the long mail, but I have been having some
trouble with my gromacs simulations lately.
My system consists of two popypeptide chains and a small ligand (or
drug like compound). I obtain the required gromacs topologies for the
ligand/drug from PRODRG dundee server. The steps I use for a MD
simulation using gromacs is briefly as follows:
1) get ligand file with required polar hydrogens and gromacs ligand
.itp file from prodrg server
2) run pdb2gmx using the gmx force field and spce water
3) correctly update the protein topology file to include ligand itp
file header, number of ligand molecules and also make sure the output
file from pdb2gmx contains the necessary ligand coordinates
3) set up box around this system, fill box with solvent (water),
neutralize system using genion
4) set up files to run energy minimization on system, run energy minimization
5) set up files to run position restrained dynamics and run position
restrained dynamics
6) setup up files and run Molecular dynamics on the system for ~ 10 ps
The above set up worked with one of the protease-ligand complex I was
testing, but had been failing for another viral protease.
This is not a bad start, but check out the advice about NPT and NVT
equilibration here
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation
The original protease pdb file that I used for the above simulations
has a small segment missing from chain A. This loop segment was highly
disorderd in the cystal structure hence, coordinates for this 7
residue segment is missing in the pdb file. This missing segment is no
where near where the ligand is bound on the protease. Does a missing
segment cause problems during siumlations?
The problems you're encountering are consistent with a non-physical
combination of topology and actual configuration. Depending what you did
with pdb2gmx, you may find that your topology has a very long bond here,
or that you have left chemical nonsense here. Either way, the best
solution will be to add in these residues by hand with some structure
building software, or to cap these mid-sequence-termini suitably.
Another general question on the genion function:
Is there a way I could not have genion be interactive. My systems
usually have a protein, a ligand and water, and I always choose group
13 (SOL) as the selection after running genion. I am asking this
because there are times when I want to run the same protein with
several different ligands and I would like a script to run through all
gromacs steps and not have a particular step be interactive.
http://wiki.gromacs.org/index.php/Making_Commands_Non-Interactive
Mark
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