AMBER Archive (2005)

Subject: RE: AMBER: minimize a ptraj average pdb structure

From: Vineet Pande (pande_vineet_at_hotmail.com)
Date: Wed Feb 09 2005 - 04:05:14 CST

>Hi, I have obtained an average structure for a protein
>in water. Now the question is how to minimize the
>average structure. I suppose that I should limit the
>number of steepest descent (NCYC) while keeping the
>average water molecule. Can people give some
>suggestions based on their experience?

Since you don't want the structure to change that much, in my opinion you
could simply control it by switching rmsd of gradients....another opinion is
to proceed with a gradual progressive minimization, like minimizing first
hydrogens, then side chains and then all the solute with backbone fixed by a
force constant. In this last step you could choose an RMSD value say
0.1......and not 0.0001.....you will then have just a clean structure,
without any bumps, that is perhaps you need..
Cheers
V

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