On Thu, Sep 30, 2010, Francesco Pietra wrote:
>
> My task is preparing prmtop/inpcrd for a peptide containing
> phenylalanine amide. This is why I tried to get prepin/frcmod files to
> feed to leap along with the pdb file of the peptide. Could you please
> suggest a promising move from here?
Use the mol2 file instead of prepi; we would like to retire prepi anyway,
since it is an Amber-only format, whereas mol2 is widely used.
>> These prepin and frcmod file are not accepted by Chimera, while VMD
>> shows a highly deformed structure (much too long C=O bond, phenyl
>> hydrogens out of plane and ring distorted; NH3 also distorted.
What options did you use in VMD? I don't see anything obvious that would
allow VMD to read an Amber prepi file. What happens if you convert the prepi
file back to mol2 or pdb format using antechamber?
....dac
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Received on Thu Sep 30 2010 - 07:30:05 PDT
