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

majid hasan pu_majidhasan at yahoo.com
Tue Apr 19 21:39:15 CEST 2011 

Yea, sure, thanks.

Majid



________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Gromacs Users' List <gmx-users at gromacs.org>
Sent: Tue, April 19, 2011 12:09:06 PM
Subject: Re: [gmx-users] atomname2type.n2t file for CNT in amber99



majid hasan wrote:
> Actually, I just restarted my computer, and now it worked. When I create the 
>topology file using the same procedure, I get a cnt.top file with atoms C, and 
>CB, which correspond to carbons with two and three bonds.
> 

Then it sounds like something in your shell environment is not set properly, 
either sourcing the wrong GMXRC or setting PATHs or something similar 
incorrectly.  Keep this in mind for the future.

-Justin

> Thanks for your help,
> Majid
> 
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Gromacs Users' List <gmx-users at gromacs.org>
> *Sent:* Tue, April 19, 2011 11:47:44 AM
> *Subject:* Re: [gmx-users] atomname2type.n2t file for CNT in amber99
> 
> 
> 
> majid hasan wrote:
>  > 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
>  >
> 
> You don't need to account for every possible atom, just what your system deals 
>with.  Ideally, the .n2t file would be setup such that any molecule would have 
>its topology properly generated, but that is a rather complex (and perhaps 
>unattainable) task.
> 
> If you send me your coordinate file and Amber99 .n2t file (off-list) I will try 
>to debug what's going on.
> 
> -Justin
> 
>  > Thanks,
>  > Majid
>  >
>  >
>  > ------------------------------------------------------------------------
>  > *From:* Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>  > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org 
><mailto: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<http://vt.edu> <http://vt.edu> | (540) 231-9080
>>  http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>  >
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> -- ========================================
> 
> 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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-- ========================================

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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