AMBER Archive (2004)

Subject: RE: AMBER: how to use prep file

From: Kristina Furse (
Date: Mon Feb 23 2004 - 14:14:20 CST

There are no atom types in a pdb file, only atom names. You do need to modify
the atom names in your pdb file to match the atom names in the prep file so
that leap will be able to match them up. The order of operations in leap is to
source a leaprc file, add any new atom types (only necessary if your frcmod
includes a non-standard atom type--see addAtomTypes command in leap section of
them manual, also described in an email that came through the mailing list
this morning!), load the frcmod to extend the standard parameter list, load
the prep file to give leap a template of your new cofactor, then load the pdb
of your system of interest. If all atoms in the pdb file are either defined in
the standard amber parameters set or your new frcmod and prep, then you should
be able to save prmtop and coordat files. Watch carefully for any warnings
from leap telling you it is not matching things up correctly.
Good luck!

>===== Original Message From "Fang, Jianwen" <> =====
> Dear all,
> I have a naive question. How should I use prep and frcmod files which
I download from amber parameter database, to generate prmtop and prmcrd files
for a cofactor I have pdb file. Do I need to modify atom types in my pdb
file? Also how to
>construct a larger system which has this cofactor?
> Thanks!
> JF
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Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University

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