AMBER Archive (2002)

Subject: Re: MM-PBSA basics

From: Lepsa (lepsik_at_marilyn.uochb.cas.cz)
Date: Mon Sep 30 2002 - 02:13:16 CDT


Hi,
just a remark: I suppose you should set LIGRES and LIGPRI to 1-3 since when
generating the topology for the ligand alone you'll have it numbered
starting from "1". Am I right?

all the best,

 Martin Lepsik

> > COMREC 1-133
> > COMLIG 134-136
> > COMPRI 134-136
> > RECRES 1-133
> > RECPRI 1-133
> > RECMAP 1-133
> > LIGRES 134-136
> > LIGPRI 134-136
> > LIGMAP 134-136
>
> The numbering scheme looks ok. Perhaps you set COMPRI to 1-136 to get
> the full output also for the complex?
>