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

[majid hasan]

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 <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

========================================
-- gmx-users mailing list    gmx-users at gromacs.org
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 gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110419/74ef841d/attachment.html>