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:
http://www.gromacs.org/Documentation/File_Formats/.itp_File
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.
-Justin
Thank You,
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
