[gmx-users] atomname2type.n2t file for CNT in amber99

[majid hasan]

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

Thanks,
Majid





________________________________
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:
> 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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