That could be helpful. I notice that the sleap addhydr command requires
proper bonding. Of course, a ligand found in a PDB file generally does not
specify bonding. So, for example, all aromatic rings are connected, but
there's no indication of single/double alternation. And alcohols and
carbonyl groups might be hard to differentiate.
Does the sleap fixbond command require the presence of hydrogens? Or is it
capable of discerning valency from bond distances and angles?
Maybe my question is this: What are the limitations of the fixbond command?
On Wed, Oct 29, 2008 at 5:49 AM, David A. Case <case.biomaps.rutgers.edu>wrote:
> On Tue, Oct 28, 2008, Robert Hanson wrote:
>
> > Great, thanks. Any easy way to have an AMBER tool add the H atoms for us?
>
> Please see the "addhydr" command in sleap (Section 3.6.3 of the AmberTools
> manual).
>
> ...dac
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo.scripps.edu
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Wed Oct 29 2008 - 05:12:16 PDT
