From: Stanley Lan (
Date: Wed Sep 21 2005 - 09:37:35 CDT

Hi everyone,

>From Gromos output I got ***sxmd.dat (final coordinates) and ***rxmd1.dat,
along with the topology file(***mta.dat). I tried to convert the final
coordinates into pdb format and import it into VMD. It worked except the
whole molecule is in pieces(broken bonds, mis-connected bonds). Same thing
happend to other two visualization programs, PyMol and RasMol. I assumed
it's because the final coordinats from GROMOS doensn't have the standard
amino acid residues and the correct connection map. My boss didn't think
so. He thinks there is something wrong with my conversion program and/or

I try to prove he is wrong but I need to be able to import the gromos output
files into VMD without conversion. Any comments/suggestions will be

Is there any GROMOS archive with string search function for me to search
this kind of questions/answers?