Dear Jason,
I sent you the pdb file and other lib file to your private email.
Thank you.
Chinsu
On Thu, May 19, 2011 at 7:18 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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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> > > 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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>
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Received on Fri May 20 2011 - 02:30:02 PDT
