<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div style="RIGHT: auto"><SPAN style="RIGHT: auto"></SPAN></div>
<DIV></DIV>
<DIV style="RIGHT: auto">Dear Gromacs list</DIV>
<DIV style="RIGHT: auto">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? </DIV>
<DIV style="RIGHT: auto"> </DIV>
<DIV style="RIGHT: auto">Any help in this regard would be highly appreciated.</DIV>
<DIV style="RIGHT: auto"> </DIV>
<DIV style="RIGHT: auto">Best regards,</DIV>
<DIV style="RIGHT: auto">Maryam<VAR id=yui-ie-cursor></VAR></DIV></div></body></html>