Dear all,
I have created mol2/pdb files of a chemical compound using Sirius. I
have verified these files using vmd and save them. Then, according to
the "sustiva" amber tutorial, leap was used to generate a prepin file
and then prmtop and inpcrd files. When I look at the structure from the
prepin file in xleap, the structure is good. Nevertheless, after saving
the prmtop and the inpcrd files, the structure from these files is
distorded in VMD. (Curiously if I generate a pdb file from these inpcrd
and prmtop using the command ambpdb, the structure seems good in
VMD...). After a simple minimization, the rst files is bad too in VMD
and I have high energies (notably for 1-4 EEL).
Which strategy do you classically use to create your initial structure
files (for compound without amino acid) to have good inpcrd/prmtop
files? Thanks.
Best regards,
Baptiste
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Received on Tue Sep 21 2010 - 03:00:05 PDT
