[AMBER] discontinuous residues

From: Jio M <jiomm.yahoo.com>
Date: Tue, 1 Jun 2010 00:05:02 -0700 (PDT)

SORRY FOR PREVIOUS MAIL... I HAVE ATTACHED A TEXT FILE



Dear Amber Users,



Can anybody please suggest that whether I can do eq dynamics for discontinuous residues on pdb file like in attached file my.pdb



here two problems are there:



1) If I dont insert TER between discontinued residue AMBER makes a bond between far residues like 495 and 70



2) If I insert TER between discontinued residues then AMBER considers

and adds missing atom OXT. OXT is not desired as CO is free end.

here no bond is formed as expected between far residues



3) Also if I remove added OXT atoms then the discontinous residues, as

they are not bonded, will fly away during dynamics and it is not good

to put positional restraints.

So please suggest is it possible to dynamics in this case or I should consider the full sequence....



thanks and regards,

JIomm






      

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Received on Tue Jun 01 2010 - 00:30:04 PDT
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