[gmx-users] miscelle formation using ligands only

[Justin Lemkul]

On 9/14/15 11:18 AM, Chetan Puri wrote:
> i tried to prepare a topolgy file for my ligands and it contained following
> things,
> #include "gromos43a1.ff/forcefield.itp"
> #include "drg1.itp"
> #include"drg2.itp"
> #include"drg3.itp"
> #include "gromos43a1.ff/spc.itp"
>
> [system]
> miscelle
> [molecules]
> 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:

http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation
http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents

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

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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