Actually, I just restarted my computer, and now it worked. When I create the topology file using the same procedure, I get a cnt.top file with atoms C, and CB, which correspond to carbons with two and three bonds.
Thanks for your help, Majid ________________________________ From: Justin A. Lemkul <[email protected]> To: Gromacs Users' List <[email protected]> Sent: Tue, April 19, 2011 11:47:44 AM Subject: Re: [gmx-users] atomname2type.n2t file for CNT in amber99 majid hasan wrote: > Just a little addition to my previous reply: if I run the same procedure with >oplsaa, it works. Now in Oplsaa, I added following two lines in already >existing >.n2t lines, > CA opls_239 0 12.011 3 C 0.142 C 0.142 C 0.142 > CA opls_239 0 12.011 2 C 0.142 C 0.142 > But oplsaa also has a bunch of other atoms named opls... , but I guess these >don't matter because nanotube only has Carbon bonded with 1,2, or 3, atoms, so >I >only added three lines for these carbons in amber99.n2t > You don't need to account for every possible atom, just what your system deals with. Ideally, the .n2t file would be setup such that any molecule would have its topology properly generated, but that is a rather complex (and perhaps unattainable) task. If you send me your coordinate file and Amber99 .n2t file (off-list) I will try to debug what's going on. -Justin > Thanks, > Majid > > > ------------------------------------------------------------------------ > *From:* Justin A. Lemkul <[email protected]> > *To:* Discussion list for GROMACS users <[email protected]> > *Sent:* Tue, April 19, 2011 10:40:53 AM > *Subject:* Re: [gmx-users] atomname2type.n2t file for CNT in amber99 > > > > majid hasan wrote: > > Dear All, > > > > In an attempt to create CNT topology with g_x2top and amber99, I was > getting >this error: no or incorrect atomname2type.n2t file found. So I tried to create >a >atomname2type.n2t file for CNT in Amber99. My coordinate file is of this form: > > UNNAMED > > 400 > > 1TUB CA 1 0.392 0.000 0.000 > > so I opened oplsaa's .n2t file, and replaced all the entries with these >three lines: > > CA C 0 12.011 3 C 0.142 C 0.142 C 0.142 > > CA CA 0 12.011 2 C 0.142 C 0.142 > > CA CB 0 12.011 1 C 0.142 > C, CA, CB are all listed in >atomtypes.atp file in Amber as: > > C 12.01000 ; sp2 C carbonyl group > > CA 12.01000 ; sp2 C pure aromatic (benzene) > > CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction > > > > > > But when I run the g_x2top, I still get the same error. > > > > And where is this .n2t file located? It needs to be in the amber99.ff >directory to actually work, and you need to provide this force field's name in >your g_x2top command, which unfortunately you have not posted. > > -Justin > > > Any help is much appreciated. > > > > Thanks, > > Majid > > > > -- ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu<http://vt.edu> | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- gmx-users mailing list [email protected] ><mailto:[email protected]> > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or >send it to [email protected] ><mailto:[email protected]>. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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