[gmx-users] atomname2type.n2t file for CNT in amber99
pu_majidhasan at yahoo.com
Tue Apr 19 20:34:05 CEST 2011
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
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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:
> 1TUB CA 1 0.392 0.000 0.000
> so I opened oplsaa's .n2t file, and replaced all the entries with these three
> 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.
> Any help is much appreciated.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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