<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">http://www.gromacs.org/Documentation/Errors</a></div><div><br></div><div>Alan</div><div><br></div><div class="gmail_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="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div>
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" target="_blank">alanwilter@gmail.com</a><br>Date: Tue, 24 Aug 2010 15:22:34 +0100<br>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">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>
</div>
<br></div></div><div class="im">--
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a> </div></div>
<br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br><br clear="all"><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/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>
</div>