[gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

Justin Lemkul jalemkul at vt.edu
Mon Sep 23 03:00:59 CEST 2013

On 9/22/13 8:54 PM, Nilesh Dhumal wrote:
> Sorry to send email directly to your email address. Because of attachments
> it not going through gmx_users.

The proper protocol is to post the files via publicly accessible URL so that 
anyone interested in helping may assist.

> attached the topology file p2.top,
> force field file glu-emi_lopes.itp and etso4.itp
> molecule files emi.itp and ets.itp file.
> I updated ffoplsaa.itp file as
> #include "glu-emi_lop.itp"
> #include "etso4.itp"
> #include "emi.itp"
> ;#include "glu-emi_lop-modify.itp"
> ;#include "dmso-nilesh.itp"
> ;#include "ffoplsaanb.itp"
> ;#include "ffoplsaabon.itp"
> ;#include "pf6_opls.itp"
> ;#include "solvent.itp"
> ;#include "bmi1.itp"
> ;#include "acetate.itp"
> ;#include "pf6.itp"
> #include "ets.itp"
> ;#include "water-flexiable.itp"

I'm not willing to hack my own force field files to make this work.  If you can 
provide a clean version, i.e. via a complete directory of modified files and/or 
post-processed topology from grompp -pp, that would be more useful and less 

Note that you did not send the coordinate file, which is critical information.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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