[gmx-users] .n2t file for ssDNA
pu_majidhasan at yahoo.com
Fri Apr 8 23:58:35 CEST 2011
But with pdb2gmx, after selecting force field and water model, I get this error:
Fatal Error: Residue 'DA3' not found in residue topology (on selecting oplsaa),
and when I selected amber99, I got following fatal error: there is a dangling
bond at at least one of the terminal ends and the force field doesn't provide
terminal entries or files. Edit a .n.tdb and/or .c.tdb file.
I also tried Amber, and Oplsaa forcefields on a different dna.pdb file, and got
missing residue errors.
Any help would be much appreciated.
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Fri, April 8, 2011 12:54:38 PM
Subject: Re: [gmx-users] .n2t file for ssDNA
majid hasan wrote:
> Dear All,
> I am trying to simulate the interaction between DNA, and CNT. But when I try to
>create the toplogy file with command
> g_x2top -f ssdna.gro -o ssdna.top -ff select, I get the following error: Fatal
>error: Could only find a forcefield type for 119 out of 287 atoms
> I am using the oplsaa forcefield, and I suspect it is because atomname2type.n2t
>file doesn't contain all the possible bonds in it. Copy of my .n2t file is
>attached with the message. Could you please guide me how to add all these
> possible bonds in my .n2t file?
That would be a very time-consuming exercise, and likely (certainly) g_x2top is
not the best tool for this job, for several reasons, the most obvious being that
a number of force fields (AMBER and CHARMM, at least) have native support for
nucleic acids via pdb2gmx.
g_x2top can certainly create a topology for a CNT, but it requires basically one
line, since the geometry is all the same. Then just #include your cnt.itp file
in your system topology and you're done.
> I also downloaded the ffoplsaanr, ffoplsaano, from user contributed gromacs
>forcefields, but these packages also don't have .n2t file.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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