AMBER Archive (2003)

Subject: mm_gbsa question

From: Javier Cuervo (jcuervo_at_sciences.sdsu.edu)
Date: Tue May 27 2003 - 19:49:18 CDT

Dear amber users,

I am trying to run a mm_gbsa calculation using the decomposition by
residue scheme. I did generate succesfully the topology files and
snapshops for complex, rec and ligand, but when I try running the energy
calculation I got the following error :

Can't use an undefined value as an ARRAY reference at
/home/programs/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1234.

(It seems to me is something related with MS card (??) )

and the las thing written in the .log file is:

=>> Reading files
    Reading 2kai-sta_com.all.out
    Reading 2kai-sta_rec.all.out
    Reading 2kai-sta_lig.all.out
=>> Treat special parameters

and not "_statistics.out" file is written and nothing (but MM GB MS) is
written in the "_all.out" files.

My input file looks as follows:

@GENERAL
#
PREFIX 2kai-sta
PATH ../snapshots/
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ../../../2kai.top
RECPT ../2kai-rec.top
LIGPT ../2kai-lig.top
#
GC 0
AS 0
DC 1
#
MM 1
GB 1
PB 0
MS 0
#
NM 0
#

@DECOMP
#
DCTYPE 2
#
COMREC 38-41 56-57 99-99 101-101 104-104 148-148 150-150
152-152 174-174 192-198 212-217 226-226 228-228
COMLIG 256-263 279-279 281-284
COMPRI 38-41 56-57 99-99 101-101 104-104 148-148 150-150
152-152 174-174 192-198 212-217 226-226 228-228 256-263 279-279 281-284
RECRES 38-41 56-57 99-99 101-101 104-104 148-148 150-150
152-152 174-174 192-198 212-217 226-226 228-228
RECPRI 38-41 56-57 99-99 101-101 104-104 148-148 150-150
152-152 174-174 192-198 212-217 226-226 228-228
RECMAP 38-41 56-57 99-99 101-101 104-104 148-148 150-150
152-152 174-174 192-198 212-217 226-226 228-228
LIGRES 11-18 34-34 36-39
LIGPRI 11-18 34-34 36-39
LIGMAP 256-263 279-279 281-284

@GB
#
IGB 2
SALTCON 0.00
EXTDIEL 80.0
#
SURFTEN 0.0072
SURFOFF 0.00

Can anybody please tell me what I am doing wrong?

I apologize for such big e-mail

Regards

Javier Cuervo
Graduate Student
Computational Sciences Research Center
San Diego State University