Dear Thomas and Jason,
Please find attached here the leap_log file and the frcmod file.
Thank you.
Chinsu
On Thu, May 19, 2011 at 12:16 PM, Thomas Cheatham <tec3.utah.edu> wrote:
>
> > I used xleap to create these prmtop and inpcrd files for the NDM
> molecule.
> > Because my ndm molecule contains 3 Zinc atoms which are not defined atom
> > types in AMBER, I created them as non-standard residues using the
> tutorial
> > A1 (advanced version) from Dr. Walker.
> >
> > I followed the steps in the tutorial. The new atom types are HIZ (His56),
> > HIA (His95), HIO (His125), CYM (Cys144), and CL (clorua ion) lib. The
> > charges for these atoms were Mulliken charges taken from Gaussian
> running.
> > And all the Zn parameters are from Ryde 1995 and Dr. Walker's thesis.
>
> It would be wonderful if you could tell us the commands you used in LEaP
> to create the prmtop. It is highly unusual for the "number of atoms per
> molecule" section of the prmtop to get altered. We need to understand if
> LEaP made a mistake or if the file was editted by hand.
>
> For us to debug, we need to understand the sequence of commands. The
> leap.log file provides most of the information; better is the sequence of
> commands and files ( *.mol2, frcmod*, ...) loaded.
>
>
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Received on Wed May 18 2011 - 22:00:02 PDT
