<html><body><P><FONT face="Courier New" size=2>Hello Sir,</FONT></P>
<P> Greetings in the name of the lord!<BR></P>
<P> I am having one docked structure .. ie., one drug-enzyme complex in INSIGHTII software. I thought of doing the energy minimisation and simulations in Gromacs.. so i transfered the pdb corrdinates of the same complex to the gromacs and edited the .top and .gro file for my complex.. with the the .gro and .top file for my drug which i obtained from PRODRG server. But before going for the minimisation when i just looked into the gro format file back in the INSIGHTII [ie.,after pdb2gmx -f pla.pdb(only the enzyme pdb) -o pla.gro -p pla.top i edited the pla .gro and pla.top with drg.top and drg.gro file which i obtained from PRODRG server and obtained an over written pla.gro and pla.top file) then i gave editconf -f pla.gro -o pla.pdb... after that i took that pla.pdb to INSIGHTII for just checking if the complex is ok but what i noticed is that few fragments of drug were scattered (ie., few atoms like C4, C5...etc were not assigned any atomtype by gromacs .. ) what to do?,Please let me know where i went wrong</P>
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