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

Justin Lemkul jalemkul at vt.edu
Thu Sep 7 00:11:54 CEST 2017

On 9/6/17 3:46 PM, Deep kumar wrote:
> 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
> wrong.
> 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)
> output.close()
> the "net charge" of "RND" was shown to be "2".

Does that make sense?  What is RND?

> 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?

You don't need a .gro file to generate a position restraint file; as with most 
operations in GROMACS, you can use any coordinate file format here.  If you 
*really* want to use .gro, you can transform between formats with editconf.

> 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.
> "

The error here is pretty clear.  You have a bad geometry for this molecule with 
a bond length that is about 3 times longer than it really should be. 
Visualizing the coordinates should make this apparent since ATB is telling you 
exactly which bond is problematic.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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