majid hasan wrote:
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.
Then it sounds like something in your shell environment is not set properly,
either sourcing the wrong GMXRC or setting PATHs or something similar
incorrectly. Keep this in mind for the future.
-Justin
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] <mailto:[email protected]>>
> *To:* Discussion list for GROMACS users <[email protected]
<mailto:[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> <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> -- gmx-users mailing list [email protected]
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-- ========================================
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]
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--
========================================
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
========================================
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