Hi, I asked the authors of the gmx amber ports what the desired behavior would be. For the time being I committed the fix, but it only gets activated when you have the env.var. GMX_FFRTP_TER_RENAME set.
Berk From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now Date: Tue, 24 Aug 2010 20:48:05 +0200 Hi, I have made a fix, but am now wondering if we actually want to fix this. HIE is not a standard pdb residue name. A file with HIS-HIS-HIS would work. HIE is an Amber name and in that case one might say that you should use: NHIE-HIE-CHIE. But I don't know what the Amber program would support for input. PS NHIE is now listed incorrectly as NHISE in residuetypes.dat, so NHIE-HIE-CHIE won't work. I'll at least commit a fix for that. Berk From: alanwil...@gmail.com Date: Tue, 24 Aug 2010 18:06:45 +0100 Subject: Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now To: gmx-users@gromacs.org 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-d748bSource 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 <g...@hotmail.com> wrote: Hi, I fixed it. Thanks for the fast test and the complete instructions, Berk From: alanwil...@gmail.com Date: Tue, 24 Aug 2010 15:22:34 +0100 To: gmx-users@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 -- 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 gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. 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<< -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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