[gmx-users] problem with calculating SASA

[Justin A. Lemkul]

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 <jalemkul at vt.edu>
> *To:* Maryam Hamzehee <maryam_h_7860 at yahoo.com>; Discussion list for 
> GROMACS users <gmx-users at 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

========================================