[gmx-users] OPLSAA and TOPOLBUILD, regarding

[Justin Lemkul]

On 1/24/18 5:45 AM, RAHUL SURESH wrote:
> I want to perform a Ligand-protein interaction in OPLSAA ff. The
> topolbuild-1.3 package is used to generate lig.gro lig.log lig.top
> fflig.itp and posrelig.itp files.
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> In case of fflig.itp it contains
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> *; topolbuild version 1.3; Command line:;     ./topolbuild -n chu -dir
> /home/viji/ALZ-PRION-THC/topolbuild1_3/dat/gromacs -ff oplsaa;#define
> _FF_OPLS#define _FF_OPLSAA#define _FF_USER[ defaults ];nbfunc
> comb-rule      gen-pairs     fudgeLJ      fudgeQQ  1
> 3               yes             0.5     0.5#include "ffoplsaanb.itp*"
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> where #define stats are outdated in latest version of gromacs.
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> Now is this .itp file is enough to perform the ligand-protein interaction?
> If not where can I generate or how can I make any most suitable itp file
> for opls ff.
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> Any detailed explanation will be most useful in this case. Please

You don't want a [defaults] directive in your ligand .itp file, because 
it will clash with the parent force field, anyway. Get rid of that 
section or else you'll get fatal errors from grompp.

-Justin

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Justin A. Lemkul, Ph.D.
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