[gmx-users] OPLSAA and TOPOLBUILD, regarding

[Ray, Bruce D]

On Jan 24, 2018, at 5:45 AM, RAHUL SURESH <drrahulsuresh at gmail.com> wrote:

> Date: Wed, 24 Jan 2018 16:15:29 +0530
> From: RAHUL SURESH <drrahulsuresh at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] OPLSAA and TOPOLBUILD, regarding
> Message-ID:
> 	<CAAtfiTuZVXnNeWyGcVYcfvScm-d_SyarYLia=bJzv2W9hotRmg at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
> 
> 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.
> 
> 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*"
> 
> where #define stats are outdated in latest version of gromacs.
> 
> 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.
> 
> Any detailed explanation will be most useful in this case. Please
> 
> Thank you
> 
> -- 
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*


Assuming that the command specified a molecule named chu, the file should have been
ffchu.itp   This file is basically useless anymore.
The file chu.top is also generated by the topolbuild command and should be renamed
chu.itp before editing.  You will need to use a text editor to remove from that file
the line near the top of the file that reads

     #include "ffchu.itp"

and all lines near the bottom starting with the line that reads

     ; Include water topology

to the end of the file.  The line removed from the top of the file is unnecessary.
The lines near the bottom or some similar appropriate set of lines will need to go
into an *.top file in which this file is given in a statement #include chu.itp 
Please see the appropriate Gromacs manual for the version of Gromacs you are
using for proper construction of such a *.top file.


-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St., Rm. LD-061
Indianapolis, IN  46202