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

majid hasan pu_majidhasan at yahoo.com
Tue Apr 19 20:43:19 CEST 2011

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


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:
>   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 
> 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.
> Thanks,
> Majid

-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

-- gmx-users mailing list    gmx-users at gromacs.org
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/20110419/46feeb35/attachment.html>

More information about the gromacs.org_gmx-users mailing list