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.
-Justin
I also downloaded the ffoplsaanr, ffoplsaano, from user contributed gromacs
forcefields, but these packages also don't have .n2t file.
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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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