[gmx-users] problem with calculating SASA

Justin A. Lemkul jalemkul at vt.edu
Mon Jan 30 13:04:52 CET 2012

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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