Dear all
I have very simple question and its related to minimization of protein
structure in solvent system by running min1 and min2 steps given in amber
tutorial.
I have modeled pentamer protein structure with total residues 1505 by using
Modeller 9.9, it is ion channel containing LBD and TMD alpha helical
structures, after checking stereochemical properties i found all values
lying within limit except about 50-60 steric clashes and energy profile
being higher too. I have minimized it through amber and got rid from bad
contact as well lowered energy profile, but i got poor phi psi plot. Before
minimization there was no residue in disallowed region and most favoured
residues were more than 90% but after amber minimization it has lowered to
85.6% most favoured and 0.9 % disallowed and 0.9% generously disallowed.
I have some confusion in this regard: first that it has water soluble (LBD)
and lipid soluble (TMD) parts both in one so is it reasonable to solvate
whole protein in water box and minimize? 2nd in homology modeling do we
count procheck results after minimzation or before minimization?
Looking forward for your valuable comments
Regards
--
MUSTAFA BUGHIO
Junior Research Fellow
Lab # P-133
Computational Medicinal Chemistry and Drug Design
Panjwani Center For Molecular Medicine and Drug Research, International
Center for Chemical Sciences, University of Karachi, Karachi 75270
Pakistan, +923313425010
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Received on Mon Aug 15 2011 - 10:00:02 PDT
