<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, thanks a lot.</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> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Sat, April 9, 2011 3:05:48 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Naming of DNA residues, and structure of .pdb file<br></font><br>
<br><br>majid hasan wrote:<br>> Dear All,<br>> <br>> I am trying to make sure that the names of dna residues in my .pdb file match with .rtp file in the Amber forcefield. I looked up the residuetypes.dat file (attached), and it gives the names for DNA residues, which are of the form, DX, DX3, DX5, DXN (X=A,C,T,G). So if I have a residue X, then what is the difference between DX, DX3, so on i.e when do I name residue X as DX, and when as DX3, and so on?<br>> <br><br>DX = normal residue<br>DX5 = 5' end<br>DX3 = 3' end<br><br>> Moreover, can anyone explain me the format of pdb file (attached) i.e what do different columns represent, so I can change the names of residues without making any error?<br>> <br><br><span><a target="_blank" href="http://www.wwpdb.org/documentation/format32/sect9.html">http://www.wwpdb.org/documentation/format32/sect9.html</a></span><br><br>-Justin<br><br>> Thanks,<br>> Majid<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]<a target="_blank" href="http://vt.edu">vt.edu</a> | (540) 231-9080<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><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>.<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></div></div><div style="position:fixed"></div>
</div></body></html>