Maryam Hamzehee wrote:
Hi
Many thanks for your email, the question is that topology file (*.top)
has not DNA, if I want to produce the tpr file I need a top file
containing both DNA and protein; How can I edit my top file in oredr to
include DNA in my top file.
Then you need to incorporate the DNA topology into the system topology, as you
would for any other molecule. The easiest way to do this is to:
1. Create a separate coordinate file with just your DNA in it
2. Run pdb2gmx on the new DNA coordinate file and obtain a DNA .top file
3. Edit the .top file to make it an .itp by removing the unnecessary directives
(see the wiki)
4. #include the new DNA .itp file in the existing system .top
-Justin
Cheers,
Maryam
------------------------------------------------------------------------
*From:* Justin A. Lemkul <jalem...@vt.edu>
*To:* Maryam Hamzehee <maryam_h_7...@yahoo.com>; Discussion list for
GROMACS users <gmx-users@gromacs.org>
*Sent:* Monday, 30 January 2012 3:34 PM
*Subject:* Re: [gmx-users] problem with calculating SASA
Maryam Hamzehee wrote:
> Dear Gromacs list
> I am trying to calculate the surface area for my DNA-protein complex
using do_dssp or g_sas. But when I convert the pdb file to *.gro file,
the topology file *.top has only protein molecule and DNA is not
included, how can I edit the topology file and include DNA in order to
be recognizable for the system. I tried the do_dssp but the surface area
for DNA has not been calculated. It should be noted that my DNA has
double strand consists of 8 nucleotides. Is it necessary to include 2
DNA in molecule type section of topology file?
>
Yes. If you ran any simulation, the inclusion of the DNA should have
been required (otherwise you'd get lots of nasty fatal errors). But in
any case, you need a .tpr file that describes the whole system, which is
assembled from grompp using a matching coordinate file and topology.
-Justin
-- ========================================
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
========================================
--
========================================
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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