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Hi,<br><br>I have made a fix, but am now wondering if we actually want to fix this.<br>HIE is not a standard pdb residue name.<br>A file with HIS-HIS-HIS would work.<br>HIE is an Amber name and in that case one might say that you should use:<br>NHIE-HIE-CHIE.<br>But I don't know what the Amber program would support for input.<br><br>PS NHIE is now listed incorrectly as NHISE in residuetypes.dat,<br>so NHIE-HIE-CHIE won't work. I'll at least commit a fix for that.<br><br>Berk<br><br><hr id="stopSpelling">From: alanwilter@gmail.com<br>Date: Tue, 24 Aug 2010 18:06:45 +0100<br>Subject: Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now<br>To: gmx-users@gromacs.org<br><br><div>I am using gmx 4.5 d748b.</div><div><br></div>Thanks Berk, it seems to be working ... for DNA.<div><br></div><div>But this one is broken (and it was working before): HHH is tripetide Hie-Hie-Hie.</div><div><br></div><div>
pdb2gmx -f HHH.pdb -o agHHH.pdb -p agHHH.top -ff amber99sb -water none</div><div><br></div><div>[snip]</div><div><div>Identified residue HIE1 as a starting terminus.</div><div>Identified residue HIE3 as a ending terminus.</div>
<div>8 out of 8 lines of specbond.dat converted successfully</div><div><br></div><div>-------------------------------------------------------</div><div>Program pdb2gmx, VERSION 4.5-beta3-dev-20100824-d748b</div><div>Source code file: /Users/alan/workspace/gromacs/src/kernel/pdb2top.c, line: 916</div>
<div><br></div><div>Fatal error:</div><div>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.</div><div>For more information and tips for troubleshooting, please check the GROMACS</div>
<div>website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a></div><div><br></div><div>Alan</div><div><br></div><div class="ecxgmail_quote">On 24 August 2010 15:30, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>></span> wrote:<br>
<blockquote class="ecxgmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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Hi,<br><br>I fixed it.<br>Thanks for the fast test and the complete instructions,<br><br>Berk<br><br><hr>From: <a href="mailto:alanwilter@gmail.com">alanwilter@gmail.com</a><br>Date: Tue, 24 Aug 2010 15:22:34 +0100<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Subject: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now<div><div></div><div class="h5"><br><br>Hi there, in special Berk.<div>
<br></div><div>So pdb2gmx may be working with HIS and variants for oplsaa but now, something that was working before is failing:</div><div><br></div><div><div>wget -c "<a href="http://www.pdbe.org/download/1BNA" target="_blank">http://www.pdbe.org/download/1BNA</a>" -O 1BNA.pdb</div>
<div>grep 'ATOM ' 1BNA.pdb >| DNA.pdb</div><div><br></div><div><div>cat << EOF >| SPE.mdp</div><div>define = -DFLEXIBLE</div><div>integrator = md</div><div>nsteps = 0</div>
<div>dt = 0.001</div><div>constraints = none</div><div>emtol = 10.0</div><div>emstep = 0.01</div><div>nstcomm = 1</div><div>ns_type = simple</div>
<div>nstlist = 0</div><div>rlist = 0</div><div>rcoulomb = 0</div><div>rvdw = 0</div><div>Tcoupl = no</div><div>Pcoupl = no</div>
<div>gen_vel = no</div><div>nstxout = 1</div><div>pbc = no</div><div>nstlog = 1</div><div>nstenergy = 1</div><div>nstvout = 1</div><div>nstfout = 1</div><div>nstxtcout = 1</div>
<div>comm_mode = ANGULAR</div><div>continuation = yes</div><div>EOF</div></div><div><br></div><div><div>pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p DnaAmberSBGMX45</div><div>[snip]</div></div><div>
<div>8 out of 8 lines of specbond.dat converted successfully</div><div>[1] 42209 segmentation fault pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p </div><div><br></div></div>with 5e347 it worded fine, i.e, it opens files</div>
<div><br></div><div><div>Opening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/aminoacids.arn</div><div>Opening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/dna.arn</div>
<div>Opening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/rna.arn</div></div><div><br></div><div>and proceed.</div><div><br></div><div>Alan<br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>
Department of Biochemistry, University of Cambridge. <br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/%7Eawd28" target="_blank">http://www.bio.cam.ac.uk/~awd28</a><<<br>
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Department of Biochemistry, University of Cambridge. <br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/%7Eawd28" target="_blank">http://www.bio.cam.ac.uk/~awd28</a><<<br>
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