My 2 cents opinion:
Try modelling the missing parts till you get a good structure first. This will save you a lot of trouble. I am not sure if swisspdb viewer does modeling of missing residues (i guess thats why you're getting bonds of 6 angstrom between some residues).
Once you insert the missing residues using the viewer, you have to use swiss-model to repair the structure. There are other tools for building the missing residues but swisspdb-viewer/swiss-model is the easiest to use.
Symon
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________________________________________
From: Jonathan Gough [jonathan.d.gough.gmail.com]
Sent: Tuesday, April 23, 2013 1:47 PM
To: AMBER Mailing List
Subject: [AMBER] Is there a trick to fix a poor structural feature?
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?
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)
any insight or pointing in the right direction would be appreciated.
Thanks,
JOnathan
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Received on Thu Apr 25 2013 - 08:30:03 PDT
