[gmx-users] D-form amino acids

[Regina R. Monaco, Ph.D.]

HI All-

	I am trying to submit a calculation to GROMACS on a hexapeptide 
composed of D-form amino acids. My input structure file is in the  .mol 
file format, which I cannot get any program to recognize as being 
composed of anything other than "UNK" residues. I have tried the 
(awesome) PRODRG2 (davapc1.bioch.dundee.ac.uk/prodrg/) site, but the 
.TOP and .ITP output files it generates still have all the residues 
labelled as "UNK".

	Does anyone know how I can handle this and run an MD simulation?

Thanks,
Regina Monaco