Re: [AMBER] PDB file conversion server to meet the atom type requirement

From: M. L. Dodson <>
Date: Sat, 7 Apr 2012 07:21:25 -0500

On Apr 7, 2012, at 4:15 AM, Acoot Brett wrote:

> Dear All,
> Is there a server for PDB file conversion in order to meet the atom type requirement of leap?
> Cheers,
> Acoot

The programs (either can be used, they are mostly the same) tleap and
xleap build the parameter-topology and coordinate files for an AMBER
MD simulation. They will correctly insert the appropriate atom types
according to the force field you choose. They will also place hydrogens
according to the residue name, e.g., HIE will have the hydrogens placed
appropriately for an epsilon-protonated histidine.

This is all described in detail in the manual for AmberTools. AmberTools,
along with this documentation, is available free of charge from the main
AMBER web site, . The documentation also describes in
some depth the various force fields available, and, in any case, furnish
references to the original literature. Please read this documentation to
make yourself familiar with the way AMBER simulations are set up. Many
utility programs are available to address the concerns you have raised on
the email list, whose purpose is to answer questions beyond those answered
in the documentation.

The web site also points to tutorials with worked out examples and explanations
of the reasoning behind each step in the example's preparation for, and conduct
of, simulations.

Good luck,
Bud Dodson
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
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Received on Sat Apr 07 2012 - 05:30:03 PDT
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