[gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now

Berk Hess gmx3 at hotmail.com
Tue Aug 24 16:30:20 CEST 2010


I fixed it.
Thanks for the fast test and the complete instructions,


From: alanwilter at gmail.com
Date: Tue, 24 Aug 2010 15:22:34 +0100
To: gmx-users at gromacs.org
Subject: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now

Hi there, in special Berk.
So pdb2gmx may be working with HIS and variants for oplsaa but now, something that was working before is failing:
wget -c "http://www.pdbe.org/download/1BNA" -O 1BNA.pdb

grep 'ATOM  ' 1BNA.pdb >| DNA.pdb
cat << EOF >| SPE.mdpdefine = -DFLEXIBLEintegrator               = mdnsteps                   = 0

dt                       = 0.001constraints              = noneemtol                    = 10.0emstep                   = 0.01nstcomm                  = 1ns_type                  = simple

nstlist                  = 0rlist                    = 0rcoulomb                 = 0rvdw                     = 0Tcoupl                   = noPcoupl                   = no

gen_vel                  = nonstxout                  = 1pbc                      = nonstlog = 1nstenergy = 1nstvout = 1nstfout = 1nstxtcout = 1

comm_mode = ANGULARcontinuation = yesEOF
pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p DnaAmberSBGMX45[snip]

8 out of 8 lines of specbond.dat converted successfully[1]    42209 segmentation fault  pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p 
with 5e347 it worded fine, i.e, it opens files

Opening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/aminoacids.arnOpening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/dna.arn

Opening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/rna.arn
and proceed.
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate

Department of Biochemistry, University of Cambridge. 
80 Tennis Court Road, Cambridge CB2 1GA, UK.

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