> 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 - 21:30:04 PDT
