[gmx-users] .n2t file for ssDNA

Justin A. Lemkul jalemkul at vt.edu
Fri Apr 8 21:54:38 CEST 2011

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.
> Thanks,
> Majid


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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