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 Has it been replaced by some other link or is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Well, a lot of that information is somewhat outdated, as I said.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 <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*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Some of that information is outdated, but there is a plethora of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
========================================
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