<div>I want to construct the trp file for a nanotube, I used prodrg but it could not calculate for non flat sp2 carbon(nanotube) . I used X2top to creating the top file from pdb (from Hyperchm), It only gave me the connetction, no bond and angles and others parameters. I got them from literature and put them in the top file and calculated the charge from quantum mechanics program. In topology file the charges were oredred on the cgnr group. It is on the basis of the group which sum of their charges are zero. But I dont know how I order charge for nanotube. finally how I can the topology file for carbon nanotube</div> <div>with best regards</div> <div>Ajloo<BR><BR><B><I>David van der Spoel <spoel@xray.bmc.uu.se></I></B> wrote:</div> <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">davood ajloo wrote:<BR>> Dear gmx-users<BR>> I want to classifying the charge on the basis of cgnr charge type.
How I <BR>> do it?<BR>please explain better what you want to do.<BR><BR>> Thanks a lot of<BR>> Ajloo<BR>> <BR>> __________________________________________________<BR>> Do You Yahoo!?<BR>> Tired of spam? Yahoo! Mail has the best spam protection around<BR>> http://mail.yahoo.com<BR>> <BR>> <BR>> ------------------------------------------------------------------------<BR>> <BR>> _______________________________________________<BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> Please don't post (un)subscribe requests to the list. Use the <BR>> www interface or send it to gmx-users-request@gromacs.org.<BR>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR><BR><BR>-- <BR>David.<BR>________________________________________________________________________<BR>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<BR>Dept. of Cell and
Molecular Biology, Uppsala University.<BR>Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>phone: 46 18 471 4205 fax: 46 18 511 755<BR>spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<BR>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<BR>_______________________________________________<BR>gmx-users mailing list gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it to gmx-users-request@gromacs.org.<BR>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR></BLOCKQUOTE><BR><p> __________________________________________________<br>Do You Yahoo!?<br>Tired of spam? Yahoo! Mail has the best spam protection around <br>http://mail.yahoo.com