[gmx-users] .top file for DNA-CNT

majid hasan pu_majidhasan at yahoo.com
Mon Apr 18 01:16:42 CEST 2011

Dear All,

I want to simulate DNA-CNT interaction, and reproduce the helical wrapping of 
DNA around CNT in the first step, and later study the effects of temperature, 
CNT length etc on the favorable geometries of hybrid.

I have created .top files for DNA, and CNT separately. To generate the top file 
of entire system (DNA-CNT), I added CNT in a box with DNA using genbox. But when 
I try to create .top file using pdb2gmx and Amber forcefield, I get an error 
that atom C in residue 11 C not found in rtp entry because rtp because .rtp file 
in Amber only contain dna residues, and if I use some other forcefield like 
oplsaa then dna residues won't be present. So how do I create the .top file for 
whole system i.e DNA-CNT?

Mailing list suggests that another and probably easier way of doing this is to 
create .itp file for CNT, and add it to dna.top file using #include file 
mechanism. So I wanted to ask how can I create .itp file from topology file 
(because I have the toplogy file for CNT), or do I need to create it manually 
from scratch?

Thank You,
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