[gmx-users] problem with calculating SASA

[Justin A. Lemkul]

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

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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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