On Fri, 2014-12-12 at 14:50 +0330, Atila Petrosian wrote:
> Dear amber users
>
>
>
> My system is a complex containing protein + ligand. Based on MM-PBSA
> tutorial, I have to create three gas phase prmtop and inpcrd file pairs as
> well as one for the solvated complex:
>
>
> Step 1) Protein.inpcrd / protein.prmtop
>
> Step 2) ligand.inpcrd / ligand.prmtop
>
> Step 3) complex.inpcrd / complex.prmtop
>
> Step 4) complex_ solvated.inpcrd / complex_ solvated.prmtop
>
>
>
> My protein has 2 negative charges.
>
>
>
> Which step should I do addions in? Only step 4 or steps 1, 3 and 4.
Neutralizing counterions should never be used in topologies intended for
use with PB or GB. In MM-PBSA analyses, that typically means steps 1
through 3. Step 4 should be given, to the best of your ability, the
counterions needed to mimic the experimental conditions you are trying
to model.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Dec 12 2014 - 05:00:03 PST
