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

[Berk Hess]

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: alanwilter at 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 at 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 <gmx3 at hotmail.com> wrote:







Hi,

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

Berk

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
-- 
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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-- 
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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