<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial,helvetica,sans-serif;font-size:10pt"><div>Alright.. <br><br>I actually simulated my protein for 5ns. Then I loaded the trajectory file and .gro file in vmd. Then, I extracted one of the frame and write it into pdb format, When I open it with vmd, one of the atom from a residue is connected to another atom in another residue. Things like this happens as VMD uses a distance-based bond determination heuristic. Therefore, I would need a structure file which specifies the bonds for my structure so that VMD doesn't have to guess.<br><br>So how can I generate the structure file I needed?<br><br>Thanks.<br><br>Regards,<br>Joyce<br><br></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 face="Tahoma" size="2"><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> Wednesday, October 20, 2010 2:25:26<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0.<br></font><br><br><br>Kwee Hong wrote:<br>> I executed the script at the therminal by typing<br>> perl top2psf.pl -i topol.top -o zz.psf<br>> Here, I attached my input file.<br>> <br><br>Your topology does not correspond to a MARTINI coarse-grained topology. As such, probably a bunch of the pattern matching is getting incorrect information. You cannot use top2psf.pl with this type of topology. It was created for a very specific purpose and requires that format, nothing else.<br><br>-Justin<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:* Wednesday, October 20, 2010 2:14:34<br>> *Subject:* Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0.<br>> <br>> <br>> <br>> Kwee Hong wrote:<br>> > Hi,<br>> ><br>> > I've got a top2psf.pl script from the web and used it to generate a psf file. Yet it generated some bonds to atoms with index 0 which should not occur. It causes VMD cannot load it and had a segmentation fault.<br>> > vmd > Info) Using plugin psf for structure file /home/birg/Desktop/zz.psf<br>> > ERROR)
Error reading bond information.<br>> > Segmentation fault<br>> ><br>> > I wonder am I getting the right top2psf.pl. Or is there any place I can get the latest stable version of that script?<br>> ><br>> <br>> There is only one version. Zeros are only printed if something goes wrong, i.e. you have provided the wrong input or something else has failed.<br>> <br>> Based solely on the information you've provided I cannot diagnose what has gone wrong.<br>> <br>> -Justin<br>> <br>> > Here, I attached the perl script I used.<br>> ><br>> > Thanks.<br>> ><br>> > Regards,<br>> > Joyce<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 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 mailing list <a
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