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
========================================
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