Yes, I saved this atomname2type.n2t file in amber99.ff, and my g_x2top command was: g_x2top -f cnt.gro -o cnt.top -ff select, and then I selected amber99 (4th option).
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 | (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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