[gmx-users] Simulation of CNT with Amber forcefield
Justin A. Lemkul
jalemkul at vt.edu
Mon Apr 18 22:27:28 CEST 2011
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 Has it been replaced by some other link or is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Well, a lot of that information is somewhat outdated, as I said.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.
> *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:
> Some of that information is outdated, but there is a plethora of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
> > 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.
> > 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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