VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Mar 21 2011 - 05:12:05 CDT

Hi:
I wonder whether there is experience with coming to AUTOPSF with
.inp/.rtf files generated for non-protein organic molecules with the
AMBER10's tool CHARMMGEN. The web is silent to this concern.

I am in trouble with ANTECHAMBER-CHARMMGEN for complex non-proteic
ligands. Thererore, I tried with a simple ligand, ibuprofen. Using .ac
type files (not .mol2 which caused immediately troubles to CHARMMGEN)
from ANTECHAMBER, CHARMMGEN generated .inp/.rtf files that were
accepted as topology by AUTOPSF, getting .psf/.pdb. AUTOPSF counted 34
atoms, which I corrected to 33, as they are. However, loading these
files to VMD, bond connections appear heavily altered. No more
ibuprofen.

Uncertain whether problems arising from my skipping PARATOOL (I am no
GAUSSIAN owner) can be posted here, to avoid overloading the mailing
list, I am not attaching files here. However, I would be happy to do
that if there is interest (or kindness to help)

Thanks

francesco pietra