trevor brown wrote:
Dear Mark,
Do you mean I will obtain 2 seperate .itp files for CNT and peptide. And
I already have spc.itp. Then I will write a short .top file which only
consists of include files.
Is that all what I will do?
Yes, you need topologies that describe all components of your system.
In addition, I think I should combine pdbs od CNT and peptide by
pymol,VMD etc.
Yes, since you need a complete description of your system's coordinates in a
single file.
-Justin
best wishes
trevor
On 18/01/2011 10:25 AM, trevor brown wrote:
Dear friends,
I have constructed a .top file for a CNT by g_x2top. to do this I
have added C-C interactions in .n2t file and also related ff in
.atomtypes.atp. I have also a .top file for a peptide by pdb2gmx.
My aim is to construct a simulation system in which I want to see the
adsorption.
I don't know the next steps, could you guide me for further steps?
You need to end up with a .top file that has the logical structure of
#include force field files
#include CNT.itp
#include peptide.itp
#include solvent.itp
[molecules]
CNT 1
Peptide 1
SOL 1
and a coordinate file whose molecules are ordered exactly as in the
above field, and whose atoms within molecules are ordered exactly as in
the [atoms] fields in the .itp file. Your molecule names must match
those given in the .itp files.
See the examples in section 5.7.1-5.7.3 of the manual.
Mark
My second question; I have .gro and .tp files for both CNT and
peptide, do I need any other files such as .itp or .ndx?
Last question: Do you have such a tutorial?
best wishes
trevor
--
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
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