[gmx-users] gromacs ligand topology file for "GNP"

Deep kumar deepak.choubey86 at gmail.com
Wed Sep 6 21:46:55 CEST 2017

Dear All,

I have produced the "ITP" files of the ligands using ATB server.  I am
mentioning the steps here, please let me know if you think anything is

a) uploaded the coordinates of ligand "RND" on ATB server. I chose
"heteromoelcule" molecule type.

b) Entered the "net charge" by calculating like this using chimera: (added
Hydrogen prior to calculating net charge and produced .mol2 file to
calculate the net charge)

from chimera import openModels, Molecule
from AddCharge import estimateNetCharge
from OpenSave import osOpen
output = osOpen("charge-estimates", "w")
for m in openModels.list(modelTypes=[Molecule]):
        print>>output, m, m.name, estimateNetCharge(m.atoms)

the "net charge" of "RND" was shown to be "2".

c) submitted the entry and after completion, downloaded the file as below:

>From "Molecular Dynamics(MD) files", chose "Forcefield" to be "Gromos54A7"
& "Format" to be "Gromacs", and downloaded "All Atom" ITP file.

I am running the MD on Gromacs version 5.1. I have prepared the protein
topology using "pdb2gmx" of Gromacs using "Gromos96 54A7" force field.

Please let me know if I did right or if anything else is needed to be done.

Secondly, I also need .gro file of the ligand. Can you please let me know
how can I get that. The tutorial am following (http://www.bevanlab.biochem.
vt.edu/Pages/Personal/justin/gmx-tutorials/complex/06_equil.html) says, I
have to prepare a position restraint file "posre_RND.itp" from the
"RND.gro" file, so how can I get the "RND.gro" file?

And lastly, please let me know how to generate topology of "GNP" molecule
with gromos53A6 FF. I tried ATB but it says error "
Error recorded: Unsupported bond length encountered: 0.56nm (PA-O5'). This
often indicates there is an error in the submitted structure.


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