Hello George,
The situation you mention happens typically when the structure was obtained from NMR NOE measurements. In that case, since you have a set of distances to constrain a possible structure, you cannot find a unique solution to the structure problem. A set of possible solutions are presented. We have been studying this case for a variety of proteins to determine whether the solutions presented can be thought of as representatives of an actual thermal equilibrium ensemble. Thus, we do MD on many of these structures, ONE at a TIME, and try to determine whether the initial structure appears naturally during MD. We use hydrodynamic transport properties as a proxy of structure because these provide a direct link to experiment. IF the structures are well determined, then doing explicit solvent MD on any of them will give you a representation of the fluctuating conformations as they would occur in solution. If you are interested in further discussion of this aspect of the problem, please write to me off list.
Cheers, Sergio
-----Original Message-----
From: George Tzotzos [mailto:gtzotzos.me.com]
Sent: Tuesday, September 14, 2010 6:54 AM
To: AMBER Mailing List
Subject: [AMBER] Residues with multiple conformations
Hi everybody,
I'd like to ask what is the best way to handle PDB files in which some of the residues are shown in multiple conformations.
Does it make sense to keep one conformation only removing the others arbitrarily. Or keep them all despite the warnings issued by LEAP.
Regards
George
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 14 2010 - 08:30:03 PDT
