On 23 April 2013 21:47, Jonathan Gough <jonathan.d.gough.gmail.com> wrote:
> I have a pdb (from an x-ray structure) that was missing several
> "loops"(they are floppy therefore were very disordered in the crystals).
> I used swisspdb viewer to add the residues back in but on a few of the
> "connections" it was a stretch.
>
> therefore leap warns me that
>
> WARNING: There is a bond of 6.802961 angstroms between:
> ------- .R<SER 363>.A<C 10> and .R<ARG 364>.A<N 1>
> WARNING: There is a bond of 3.723094 angstroms between:
> ------- .R<SER 990>.A<C 10> and .R<ARG 991>.A<N 1>
> WARNING: There is a bond of 4.437505 angstroms between:
> ------- .R<ALA 1197>.A<C 9> and .R<VAL 1198>.A<N 1>
>
> and (of course?) there aren't any improper torsion parameters and I get
> more warnings.
>
> the question is
>
> 1 - can I still use what I have and minimize (I think I have tried this
> several different ways and things go crazy)? If so any suggestions on how
> to go about doing it? (I tried/thought I could do it in implicit and
> explicit solvent followed by slow heating with heavy constraints and short
> times steps.)
>
> 2 - is there a "trick" to fixing what I have?
>
>
The best of its kind:
http://www.yasara.org/minimizationserver.htm
> 3 - is there a better (easier) way to build out missing residues denovo
> (letting amber build them by leaving out the residues does not work as it
> fills in the missing atoms in a straight line - not in a loop as I need)
>
>
Perhaps this server can give you better models, provided that loops are the
only part missing from your structure:
http://falc-loop.seoklab.org/
> any insight or pointing in the right direction would be appreciated.
>
> Thanks,
> JOnathan
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Wed Apr 24 2013 - 23:30:03 PDT
