[gmx-users] Overriding atom type.

[Justin Lemkul]

On 12/4/19 1:18 PM, Yogesh Sharma wrote:
> greetings Dr. Justin
>
>   I used charmm gui Input generator for ligands. these are H2O2, NO and
> Urea. I got three files for each Charmm36.itp, ligand.itp and topol. top. I
> added charmm36.itp files for each ligand under subsequent section with my
> system.itp and added #include link for  ligand.itp files in my topol file.
> Everything is working fine if, I am simulating them one by one but when
> combined, system is showing overriding atom type error for common named
> residues.
CHARMM-GUI provides a force field file that contains only the parameters 
you need for the system you have supplied it. In that way, it differs 
from a normal force field that already has everything, even parameters 
you may not need. Given this assumption that CHARMM-GUI makes, editing 
topologies it provides can be difficult. Any redundant parameters have 
to be removed if you're going to make changes to the set of files it 
provides.

Or use the CHARMM36 port (which has the full force field) and augment it 
with any new parameters that the CGenFF program (within CHARMM-GUI) came 
up with.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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