Re: [AMBER] loadPdbUsingSeq command

From: Bashford, Donald <>
Date: Tue, 14 Jun 2011 10:23:00 -0500

At Tue, 14 Jun 2011 08:27:41 -0500,
David A Case wrote:
> I'm looking into seeing if just increasing the string size would correct
> the problem, but a more basic question is this: why are you using
> loadPdbUsingSeq rather than loadPdb itself? [My personal view is that the
> loadPdbUsingSeq command should probably be deep-sixed -- we should ask
> users to edit the pdb file if they need to change the sequence. But people
> that make use of this command might want to chime in here.] But see if
> you can just use loadPdb instead.

Very often one wants to load PDB files of proteins with missing
loops. Assuming one adds TER records in the breaks, the default
behavior of loadPdb is to create charged termini, which might be a
problem. Although the really right way is to either model the loops
somehow or add neutral protecting groups, it may sometimes be
reasonable to just leave these ends with open valences. Section 3.3.2
of the AmberTools manual shows how to use loadPDBUsingSeq to do
this. I myself don't do this, except for quick trials on short files,
but maybe some people do this more seriously.

Email Disclaimer:

AMBER mailing list
Received on Tue Jun 14 2011 - 08:30:04 PDT
Custom Search