AMBER Archive (2001)

Subject: Re: How tleap does not add missing H atoms?

From: Jarrod Smith (jsmith_at_structbio.vanderbilt.edu)
Date: Mon Mar 26 2001 - 12:47:50 CST

Xiaolin Chuang wrote:
>
> Dear AMBERs,
>
> When I used tleap with command 'aa = loadpdb dna.pdb', it automatically
> added missing H atoms which I would not like.
>
> Could anyone suggest me how to setup tleap to does NOT add missing H atoms?

What if you start tleap with the -s option so that it doesn't run the
leaprc file (i.e. not load any libraries)? It will complain alot when
you load your molecule, but it should still load the atoms and let you
do a bondbydistance.

This may or may not be useful depending on what you are trying to
accomplish. 

-- 
Jarrod A. Smith
Research Asst. Professor, Biochemistry
Asst. Director, Center for Structural Biology
Computation and Molecular Graphics
Vanderbilt University

jsmith_at_structbio.vanderbilt.edu