Re: Xleap, PDB file format

From: Jarrod Smith <>
Date: Fri 26 Oct 2001 10:12:49 -0500 (CDT)

On Fri, 26 Oct 2001, Sophia Kondratova wrote:

> Hello,
> When I construct a molecule in xleap, it does not give me atom types or
> charges for the atoms, and in the tutorials on the website, for example in the
> methane tuturial, the tutorial just says to go into the table editor and fill
> in the atom types and atom charges. Is that the only way to constuct a
> molecule in xleap, where you have to manually type in charges and atom types
> in order to construct the appropriate .top and .crd files. Also where are
> these values found.

Yes, typing them in by hand is the only way (that I know of) to create a
molecule completely from scratch. If you are comfortable with the .off
file format (and are careful and double-check your work) you can do some
of this outside of leap in your favorite text editor, however.

Partial charges need to be supplied by you. Usually these are generated
with Guassian (Hartree Fock, 6-31G* ???) and RESP, if I remember
correctly. It has been quite awhile since I did that.

I usually refer to the 1994 forcefield paper (sorry, I don't have the
ref. handy) for the atom types and descriptions.
> Another question is regarding the pdb file format. What pdb file format does
> amber accept, because if I save molecules in pdb format (not proteins but
> smaller organic molecules) and I try to open it in xleap, it does not
> recognize any atom types and cannot connect the atoms.

If Leap does not know about the residue before you load the pdb file, it
cannot assign atom types. Leap has to have some way to know the identity
of the atoms in the PDB file you are loading. And as far as I know there
is no facility to automatically assign atom types for new residues.

What you need to do is go through the steps you outlined in your first
paragraph and then load the resulting residue library into leap each time
you want to use it. Make sure the residue name(s) match the residue
name(s) in the PDB file you are trying to load.

Hope that helps

Jarrod A. Smith, Ph.D.
Asst. Director, Center for Structural Biology
Research Asst. Professor, Biochemistry
Vanderbilt University
Received on Fri Oct 26 2001 - 08:12:49 PDT
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