Re: [AMBER] loadPdbUsingSeq command

From: Antonija Tomić <>
Date: Wed, 15 Jun 2011 10:02:48 +0200

Excuse me for the first part of my tleap script, this is clearly the mistake.
But my problem with loadPdbUsingSeq command still remains.

As Donald said I am using loadPdbUsingSeq command in tleap because I
want to take the middle part of my big enzyme for further calculations
and for that I need to leave these ends with open valences (I don't
want tleap to create charged termini or to add neutral protecting

So, as I thought, problem is number of characters in strings. Is there
a way to change this?


Citiram "Bashford, Donald" <>:

> 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.
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Received on Wed Jun 15 2011 - 01:30:03 PDT
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