[gmx-users] Regarding .itp file to the system

Justin Lemkul jalemkul at vt.edu
Wed Dec 9 19:01:23 CET 2015

On 12/9/15 12:57 PM, Alex Mathew wrote:
> Justin,
> Thanks for your quick reply
> so how i should proceed with .itp file as per your tutorial .gro file is
> required ,if i add "new.itp" to topol.top there might be problem that atom
> number mismatch between the conf.gro which produced for protein alone

Let's be clear about one thing: my tutorial does not say a .gro file is 
required. It simply uses default file extensions for everything because that is 
how most users go about daily business. The procedure, in general, is always the 

1. Process the protein with pdb2gmx and obtain a .top and coordinate file in 
whatever format you like.
2. Generate a ligand topology, #include its .itp file in the .top
3. Append the ligand coordinates to those of the protein from step (1); again 
format is irrelevant

Done and done.

> When i tried to load mol2 file in charmmgui it gives an error
> here is a mismatch in the order of ligand heavy atoms in between the
> sdf/mol2 file and the original PDB file.
> when i corrected mol2 file manually it shows error
> so in either way how i should proceed,?

If you already have all the parameters for it, you shouldn't have to restart 
from scratch; CHARMM-GUI allows you to upload a topology (stream file or 
rtf+prm) for the ligand.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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