[gmx-users] Simulation of CNT with Amber forcefield

[Justin A. Lemkul]

majid hasan wrote:
> Okay, so I am able to create cnt.rtp, and cnt.top file using g_x2top. 
> But g_x2top only supports OPLSAA, and GROMOS forcefield, and if I use a 
> different forcefield then I get this error: Fatal Error: No or incorrect 
> atomname2type.n2t file found,
> which is because other forcefields don't contain any .n2t files. And, I 
> don't want to create cnt.top using oplsaa/gromos because these 
> forcefields are not suitable for dna. So what is the way around i.e if I 
> can't use the same force field to construct both (cnt and dna) 
> topologies, then what do I do? 
> 
> Is any of following likely to work (though I don't think so):
> 
> 1) Create cnt.top and cnt.rtp using x2top oplsaa, and add cnt.rtp in amber?

No.  As we discussed last night, you can't combine force fields in this way.

> 2) Add an atomname2type.n2t in amber?
> 

That's a much better approach.

> Lastly, the link http://cs86.com/CNSE/SWNT.htm doesn't contain anything 
> at the moment. Has it been replaced by some other link or is 
> it permanently down? 
> 

Well, a lot of that information is somewhat outdated, as I said.  Search the 
list archive, as I suggested before.

-Justin

> Thanks,
> Majid
> 
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Mon, April 18, 2011 10:25:39 AM
> *Subject:* Re: [gmx-users] Simulation of CNT with Amber forcefield
> 
> 
> 
> majid hasan wrote:
>  > Dear All,
>  >
>  > I am doing a DNA-CNT simulation, and I am trying to generate a 
> topology of CNT using Amber99, which has been used for such systems, and 
> CNT atoms are modeled using sp2 carbon parameters.
>  >
>  > But when I try to create topology file using: pdb2gmx -f cnt.pdb -p 
> cnt.top, and Amber99 forcefield, I get this error:
> 
> Have you created an .rtp entry for your CNT?  I doubt that it's even 
> possible for cyclic molecules like this one.  pdb2gmx is only useful for 
> linear molecules composed of repeating building blocks, with limited 
> support for branching.  You may want to consult:
> 
> http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube
> 
> Some of that information is outdated, but there is a plethora of 
> information in the list archive about proper CNT topology generation.  
> Search for posts by Christopher Stiles.
> 
>  > Fatal Error: Atom C in residue C 1 was not found in rtp entry RCN 
> with 30 atoms while sorting atoms.
>  >
> 
> This answers my question above.  Your structure is being interpreted as 
> RNA. Without significant effort and perhaps code modification, pdb2gmx 
> is not likely to be useful here.
> 
>  > During the execution, it says "There are 1 chains and 0 blocks of 
> water and 1 residues with 168 atoms" after analyzing pdb file.
>  >
>  > So I suspect problem is that it reads carbon as a residue in my .pdb 
> file.
>  > If this is the problem, then how do I make sure that it reads carbon 
> as an atom and not a residue?
>  >
>  > My .pdb file has entries of the form:
>  > ATOM  1  C    C  A  1  4.039    ....
>  > ATOM  2  C    C  A  1  3.97      ....
>  >
> 
> Well, you've named your residues "C" and the component atoms "C" so 
> there's no real confusion about anything.  It's also not the source of 
> your problems.
> 
> g_x2top may be a useful program for generating a topology, or perhaps 
> other software that is entirely unrelated to Gromacs.
> 
> -Justin
> 
>  > Thanks for your help,
>  > 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> | (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

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