Date: Sun, 29 Sep 2002 19:44:52 -0700
From: Holger Gohlke
Subject: Re: MM-PBSA basics

Hi,

> I am attempting to get started with MM-GBSA on a protein-ligand
> complex. There are 136 (non-water) residues in my trajectory, with
> residues 1-133 being protein and 134-136 being ligand.
>
> I *really* have read the manual, looked at the examples, and scoured the
> e-mail reflector, but still am unclear on some basics. I want to get
> the decomposed free energy components of the ligand-protein
> interactions. I want to use just the trajectory (not 3 separate
> topology files, if possible).

Even if it is said "snapshots from the same trajectory", you need to
prepare three different types of crd files (com, rec, lig) and you need
to use three different topology files (com, rec, lig) with them. The
difference is where the coordinates come from - either from three
separate trajectories or only from the complex trajectory. But you need
three appropriate topology files in any case!

> 1) COMREC, RECRES etc.: This is clear as beer in the input file, but
> I'm still unsure if I've got it right.
> I'm assuming that, because I'm not giving 3 topology files, the
> numbering scheme is as follows:
>
> 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?

> 2) Makecrd - this is where I define ligand/receptor if using a single
> trajectory? In other words, do I need to define lstart, lstop, rstart
> and rstop if I've already done so as seen above?

Yes, you need to. I suggest generating snapshots first (only use GC = 1
in the input file), then check if your topology files fit to the
coordinates (i.e. if the structures "look good"), and finally do the
analysis.

I hope this helps - best regards

Holger