[Chimera-users] Chimera vs Amber, which one digresses from the average pdb rules?

Francesco Pietra chiendarret at yahoo.com
Mon Nov 26 00:08:16 PST 2007

Thanks. Please see below.

--- Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> On Nov 23, 2007, at 12:56 PM, Francesco Pietra wrote:
> > Here I really don't understand. With your "including recent  
> > changes" above, I
> > understand that you follow 3.0 or 3.1 PDB format. Unless you add  
> > that 3.0 and
> > 3.1 formats are exercises not to follow (the official pdb booklet I  
> > have, is V.
> > 2.3, added of V. 3.0 and V 3.1). If you follow 3.0, modification of  
> > Amber's
> > file
> As Elaine mentioned, v2.3 PDB files would place 'H' in column 14, so  
> a 4-letter hydrogen name would be something like 1HD1, whereas in  
> v3.0 they decided to just have the H start the name, producing names  
> like HD11.  The fact that Chimera still produces v2.3 hydrogen names  
> is wrong, and I have added your name to the bug-database entry for  
> producing 3.0 names, but nonetheless the PDB changeover to 3.0 only  
> happened a few months back, so most programs should be able to handle  
> both forms.

I succeed in letting LEaP (Amber9) reading pdb files written by Chimera. Which
may still be in the economy in view of "delete overlapping residues"
possibility in Chimera.

> > Finally, everything in the "classic" are is in view of MD. Even  
> > DOCK is
> > recommended as a preliminary to MD (by both Scott Brozell and D case).
> > Therefore, it is a pity - to say politely - having to spend so much  
> > effort in
> > rectifying files from pre-programs. Unless Chimera is bound to some  
> > other MD
> > suite than Amber, to which MD suite Chimera's files flow in without  
> > barriers.
> Chimera isn't "bound" to any MD suite in particular.  It simply tries  
> to produce standard PDB files.  The only software we've made a  
> conscious attempt to coordinate with is DOCK.

Yes, and that is an extremely useful coordination. However, DOCK is strictly
bound to Amber. I don't simply mean the DOCK's built-in amber_rescore, but
Scott Brozell indication to run Amber's MD after the series of dockings.

I can say again that in my opinion Chimera is a gem. I could not have done what
I have done so far in docking-MD without Chimera. Now - with side help by VMD -
I have the protein-ligand complex in a membrane, the whole solvated. Though, a
choice of different protocols when saving pdb files from Chimera ("saving for
LEaP) would speed up the work by certain users. Is it a major modification of


> --Eric
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
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