[gmx-users] miscelle formation using ligands only
jalemkul at vt.edu
Mon Sep 14 18:43:24 CEST 2015
On 9/14/15 11:18 AM, Chetan Puri wrote:
> i tried to prepare a topolgy file for my ligands and it contained following
> #include "gromos43a1.ff/forcefield.itp"
> #include "drg1.itp"
> #include "gromos43a1.ff/spc.itp"
> drg1 8
> drg2 5
> drg3 7
> sol 363408
> But since i have packed the system using PACKMOL intially there were some
> error that no. of coordintaes of gro and top file are not matching since
> intially i took no. of molecules as one for each type but later upon
> changing to the no. as in my packmol input that error had gone and new
> error is showing up
> i.e. Too few parameters in line 1 for drg2.itp
> Too few parameters in line 1 for drg3.itp
> and if i override it with maxwarn than i saw that all the ligands were
> stuck together at one place and also with some different representation .
Don't blow past error messages with -maxwarn. It is extremely dangerous and
unless you have specific knowledge that the problem is not important, don't use it.
The error messages indicate that the contents of drg2.itp and drg3.itp are
incorrect or misformatted (or perhaps that the lack of a space between #include
and the file name is causing a problem, but that's just speculation).
> so can you please help me out with this thing and also is there any other
> way by using gromacs and packing a system of different ligands (gromacs
> version 5.0.4)
gmx insert-molecules can be used to add small molecules into a system, but if
it's already built, why bother?
If you want to rebuild the system for any reason, see:
If you want commentary on the contents of your .itp files, you will need to
upload them to a file-sharing service and provide the URL. Otherwise, we're
working blind and that is not productive for anyone.
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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