AMBER Archive (2001)

Subject: Re: Xleap, PDB file format

From: David Case (case_at_scripps.edu)
Date: Fri Oct 26 2001 - 10:59:14 CDT

On Fri, Oct 26, 2001, Sophia Kondratova wrote:

>
> When I construct a molecule in xleap, it does not give me atom types or
> charges for the atoms,

Jarrod's answer was a good one. To just make a shameless plug for the
next release: amber7 will have the ability to automatically assign atom
types and charges starting from a standard pdb file, and to output residue
libraries suitable for LEaP.

This clearly won't work on "everything", but we are hoping to cover most
of organic chemistry. And it will probably still be the case that carefully
constructing a force field by hand will be better than any automated
procedure. But this should be a good start.

....dave case 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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