<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial, helvetica, sans-serif;font-size:10pt"><div>It works.</div><div>Thanks a lot</div><div style="font-family:arial, helvetica, sans-serif;font-size:10pt"><br><div style="font-family:arial, helvetica, sans-serif;font-size:13px"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br><b><span style="font-weight: bold;">To:</span></b> Gromacs Users' List <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Friday, January 14, 2011 12:18:45<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Re: pdb2gmx: segmentation fault<br></font><br><br><br>Kwee Hong wrote:<br>> Sorry. Sorry.<br>> This would be the working one. I've tested it outside my uni domain.<br>> <br>> <a
href="http://www.birg1.fbb.utm.my/joyce/protein_dock.pdb" target="_blank">http://www.birg1.fbb.utm.my/joyce/protein_dock.pdb</a> <br><br>Remove the www and it works for me.<br><br>Your .pdb file has several problems:<br><br>1. Loads of blank space at the end.<br>2. All lines are misformatted, with all columns after the chain identifier shifted by one space. In vi, use :1,$s/ B / B/g to fix it. This alleviates the seg fault.<br>3. Asn106 has its N atom labeled as residue 105.<br><br>Fixing all of the above resulted in a usable topology with Gromacs 4.5.3.<br><br>-Justin<br><br>> <<a href="http://www.birg1.bioscience.utm.my/joyce/protein_dock.pdb" target="_blank">http://www.birg1.bioscience.utm.my/joyce/protein_dock.pdb</a>> <br>> joyce<br>> <br>> ------------------------------------------------------------------------<br>> *From:* Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> *To:* Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Friday, January 14, 2011 11:57:01<br>> *Subject:* Re: [gmx-users] Re: pdb2gmx: segmentation fault<br>> <br>> <br>> <br>> Kwee Hong wrote:<br>> > Sorry, this should be correct link to download the file.<br>> >><br>> >> <a href="http://www.birg1.bioscience.utm.my/joyce/protein_dock.pdb" target="_blank">http://www.birg1.bioscience.utm.my/joyce/protein_dock.pdb</a><br>> <br>> This link also does not work.<br>> <br>> -Justin<br>> <br>> >> <<a href="http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb" target="_blank">http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb</a>><br>> >><br>>
>><br>> > Joyce<br>> ><br>> > ------------------------------------------------------------------------<br>> > *From:* Mark Abraham <<a ymailto="mailto:mark.abraham@anu.edu.au" href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a> <mailto:<a ymailto="mailto:mark.abraham@anu.edu.au" href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>>><br>> > *To:* Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>><br>> > *Sent:* Friday, January 14, 2011 11:29:45<br>> > *Subject:* Re: [gmx-users] Re: pdb2gmx: segmentation fault<br>> ><br>> ><br>> ><br>> > On 01/14/11, *Kwee Hong * <<a
ymailto="mailto:jestan1985@yahoo.com" href="mailto:jestan1985@yahoo.com">jestan1985@yahoo.com</a> <mailto:<a ymailto="mailto:jestan1985@yahoo.com" href="mailto:jestan1985@yahoo.com">jestan1985@yahoo.com</a>>> wrote:<br>> >><br>> >> Hi all,<br>> >><br>> >> I've uploaded my pdb file<br>> >> at <a href="http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb" target="_blank">http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb</a><br>> >> Maybe someone can help me to look into it and see does it has any error.<br>> >><br>> > That link does not work.<br>> ><br>> > Mark<br>> >><br>> >><br>> ><br>> <br>> -- ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT
Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>> <br>> ========================================<br>> -- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" 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/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/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 ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>> <br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- gmx-users
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