Hi, I fixed it. Thanks for the fast test and the complete instructions,
Berk From: [email protected] Date: Tue, 24 Aug 2010 15:22:34 +0100 To: [email protected] 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 -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<< -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
