AMBER Archive (2005)

Subject: AMBER: MM-PBSA error

From: MURAT CETINKAYA (cetinkayam_at_psu.edu)
Date: Mon Sep 05 2005 - 11:00:13 CDT

Dear Amber Users,

I am trying to extract the coordinates of four residues in my trajectory file
for energy analysis. So, I tried to generate snapshots in CRD format. However,
the traj_rec.crd.x files have the following output:

   77
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000

and my input file is like:

@GENERAL
PREFIX traj
PATH ./
#
COMPLEX 0
RECEPTOR 1
LIGAND 0
#
GC 1
AS 0
DC 0
#
MM 0
GB 0
PB 0
MS 0
#
NM 0
#
@MAKECRD
BOX NO
NTOTAL 77
NSTART 1
NSTOP 5
NFREQ 1
#
NUMBER_LIG_GROUPS 0
LSTART 0
LSTOP 0
NUMBER_REC_GROUPS 4
RSTART 947
RSTOP 983
RSTART 3138
RSTOP 3151
RSTART 3169
RSTOP 3179
RSTART 3443
RSTOP 3457
#
@TRAJECTORY
TRAJECTORY mdcrd
TRAJECTORY mdcrd2
#

Can anybody tell me what's going on?
Thanks in advance
Murat CETINKAYA, M.Sc.
Biomolecular Materials Lab,
Dept. of Engr. Science and Mechanics,
The Pennsylvania State University,
University Park, PA 16802
office: (814) 863 9967
web: www.personal.psu.edu/muc176
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