Do you also have the input PDBs and everything that I could just *run* leap
with to see if I get your result?
On Thu, May 19, 2011 at 12:48 AM, Chinh Su Tran To <chinh.sutranto.gmail.com
> wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu May 19 2011 - 04:30:04 PDT
