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

[Justin Lemkul]

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

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

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