[gmx-users] D-form amino acids

Regina R. Monaco, Ph.D. rocket at earthlight.com
Thu May 29 06:03:01 CEST 2003

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?

Regina Monaco

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