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

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 18 01:54:11 CEST 2011

majid hasan wrote:
> 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?

The conversion of .top to .itp is simple.  A .top is a system topology and 
contains a description of the entire system.  An .itp file describes one type of 
molecule.  To create a .itp from a .top, follow this:


Then a simple system topology is just:

#include (whatever force field)
#include "cnt.itp"
#include "dna.itp"
#include "spc.itp" (or whatever water)
#include "ions.itp" (if needed)

Finish with appropriate [system] and [molecules] directives.


> Thank You,
> 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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