I am using gmx 4.5 d748b. Thanks Berk, it seems to be working ... for DNA.
But this one is broken (and it was working before): HHH is tripetide Hie-Hie-Hie. pdb2gmx -f HHH.pdb -o agHHH.pdb -p agHHH.top -ff amber99sb -water none [snip] Identified residue HIE1 as a starting terminus. Identified residue HIE3 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully ------------------------------------------------------- Program pdb2gmx, VERSION 4.5-beta3-dev-20100824-d748b Source code file: /Users/alan/workspace/gromacs/src/kernel/pdb2top.c, line: 916 Fatal error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Alan On 24 August 2010 15:30, Berk Hess <[email protected]> wrote: > 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.mdp > define = -DFLEXIBLE > integrator = md > nsteps = 0 > dt = 0.001 > constraints = none > emtol = 10.0 > emstep = 0.01 > nstcomm = 1 > ns_type = simple > nstlist = 0 > rlist = 0 > rcoulomb = 0 > rvdw = 0 > Tcoupl = no > Pcoupl = no > gen_vel = no > nstxout = 1 > pbc = no > nstlog = 1 > nstenergy = 1 > nstvout = 1 > nstfout = 1 > nstxtcout = 1 > comm_mode = ANGULAR > continuation = yes > EOF > > 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.arn > Opening 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 <http://www.bio.cam.ac.uk/%7Eawd28><< > > -- 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 > -- 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<<
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