[gmx-users] .n2t file for ssDNA

majid hasan pu_majidhasan at yahoo.com
Fri Apr 8 21:39:38 CEST 2011

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?

I also downloaded the ffoplsaanr, ffoplsaano, from user contributed gromacs 
forcefields, but these packages also don't have .n2t file.

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