AMBER Archive (2003)

Subject: Re: question about mm_pbsa

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Sun Mar 09 2003 - 21:31:10 CST

Hi,

in the current form, the parser for the decomposition information needs
ranges in the form "x-y", where x and y are residue numbers. So for your
input on the COMLIG, COMPRI, ... lines below, you need to give "1-1"
instead just "1".

Best regards

Holger

> Hi:
> I run MD for my ligand with H2O. I want to decompose the interaction enery
> between the ligand and H2O. First, I generated the snapshots file from the
> trajectory. It works fine. Then I tried to decompose the energy, my input file
> is like:
> PREFIX dhnp-dc
> PATH ./
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> #
> COMPT ./dhnp.prmtop
> RECPT ./dhnp-wat.prmtop
> LIGPT ./dhnp-now.prmtop
> #
> GC 0
> AS 0
> DC 1
> #
> MM 1
> GB 1
> PB 0
> MS 0
> #
> NM 0
> #
> DCTYPE 2
> #
> COMREC 2-1218
> COMLIG 1
> COMPRI 1
> RECRES 1-1217
> RECPRI 1
> RECMAP 2-1218
> LIGRES 1
> LIGPRI 1
> LIGMAP 1
>
> And when I run it, I always get:
> =>> Init data
> Presuming executables of amber suite to be in /usr/local/amber7/exe
>
> =>> Reading input parameters
> Found PREFIX => dhnp-dc
> Found PATH => ./
> Found COMPLEX => 1
> Found RECEPTOR => 1
> Found LIGAND => 1
> Found COMPT => ./dhnp.prmtop
> Found RECPT => ./dhnp-wat.prmtop
> Found LIGPT => ./dhnp-now.prmtop
> Found GC => 0
> Found AS => 0
> Found DC => 1
> Found MM => 1
> Found GB => 1
> Found PB => 0
> Found MS => 0
> Found NM => 0
> Found DCTYPE => 2
> Found COMREC => 2-1218
> Found COMLIG => 1
> Found COMPRI => 1
> Found RECRES => 1-1217
> Found RECPRI => 1
> Found RECMAP => 2-1218
> Found LIGRES => 1
> Found LIGPRI => 1
> Found LIGMAP => 1
> Found DELPHI => /home/gohlke/src/delphi.98/exe.R10000/delphi
>
> =>> Checking sanity
> Checking GENERAL
> Implicit SAS calc by sander
> Checking DC
> Wrong format for decomp: 1
> But I don't know what's wrong? Anybody can help me?
>
> Thanks.
>
> Lishan 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++