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?
Any help in this regard would be highly appreciated.
Best regards,
Maryam
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