<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt"><div>Okay, I am trying AmberTools as well. Thanks Justin!</div><div><br></div><div>Majid</div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><br><div style="font-family:arial, helvetica, sans-serif;font-size:10pt"><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> Sun, April 10, 2011 10:16:57 AM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Dangling bond error for dna<br></font><br>
<br><br>majid hasan wrote:<br>> Is there any software that generates .pdb file consistent with amber forcefield requirements? I tried 3DNA, and GABEDIT, but 3DNA doesn't name residues in correct format i.e DX, and gabedit names every residue as DX3.<br>> <br><br>Perhaps xleap (part of AmberTools), but if your input has a bunch of incorrect atoms, I don't know how well it deals with replacing them. I seem to remember that it just writes new atoms and doesn't necessarily clean up the old ones, but my memory could be incorrect or the program may have been improved since last I tried it.<br><br><span><a target="_blank" href="http://ambermd.org/#AmberTools">http://ambermd.org/#AmberTools</a></span><br><br>-Justin<br><br>> Thanks,<br>> Majid<br>> <br>> ------------------------------------------------------------------------<br>> *From:* Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> *To:* Gromacs Users' List <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Sun, April 10, 2011 4:17:59 AM<br>> *Subject:* Re: [gmx-users] Dangling bond error for dna<br>> <br>> <br>> <br>> majid hasan wrote:<br>> > Sorry, the pdb file is bigger than 50k so it won't attach, so its pasted below. Output of pdb2gmx is attached.<br>> ><br>> <br>> You have numerous problems with this .pdb file:<br>> <br>> 1. All residues are listed as being the 3' end form. Your chain should start with a 5' end, include the "middle" residues, and end with a 3' form.<br>> <br>> 2. 5' ends do not have phosphate on them, per force field convention.<br>> <br>> 3. You have various incorrect atoms, and some incorrect atom names.<br>> <br>> Please refer to the dna.rtp
file for your chosen force field to understand its expectations. Then you will need to manually fix your .pdb file by renaming, replacing, or removing whatever is in conflict.<br>> <br>> -Justin<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]<a target="_blank" href="http://vt.edu">vt.edu</a><span> <<a target="_blank" href="http://vt.edu">http://vt.edu</a>> | (540) 231-9080</span><br><span>> <a target="_blank" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a></span><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><span>> <a target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></span><br><span>> Please search the archive at <a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!</span><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><span>> Can't post? Read <a target="_blank"
href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a></span><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><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>.<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></div></div><div style="position:fixed"></div>
</div></body></html>