On Thu, Apr 30, 2015, Swithin Hanosh wrote:
>
> After minimising and heating a protein-ligand complex, I found that the
> organic molecule in the protein has an unfavorable conformation that
> doesn't match with that of initial structure of the organic molecule (i.e.
> before heating), although the protein structure is intact. The pdb file
> used for creating frcmod and mol2 is sqm generated, generated after feeding
> the pdb file to the antechamber. I have attached a picture showing the
> comparison of structures (the yellow colored one is the heated and the red
> colored one is the initial structure) along with heat.out, frcmod and mol2
> file. Please explain me what is the causation of this structural change and
> way to rectify it.
It appears that our parmeterization of the organic molecule must have
problems. You are creating a ring structure (with an S-O bond(!?!)) in the
yellow that probably should not be there. The sam1.mol2 file you post indeed
has an S-O distance of 1.81 Ang., and a bond is indicated to be formed.
It's not clear how this happened. Are you sure you gave the red structure as
input to antechamber? This could be an sqm minimization problem, but it seems
very odd to me. See what happens if you use the R.E.D. server to get RESP
charges (this might already be in one of their databases, anyway).
...dac
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Received on Thu Apr 30 2015 - 08:00:02 PDT
