AMBER Archive (2009)

Subject: Re: [AMBER] MM_PBSA enquiries

From: manoj singh (mks.amber_at_gmail.com)
Date: Sun Nov 08 2009 - 09:21:12 CST

Since MM-PBSA is a implicit solvent method, you should delete solvent water
walecule (you can keep water molecule which are present in binding pocket
etc and mediating ligand binding)

When using MM-PBSA, the surface tension coefficient is 0.00542 with a
correction term 0.92. However, when doing MM-GBSA, the surface tension
coefficient with amber charges is 0.0072.

On Sun, Nov 8, 2009 at 9:53 AM, s. Bill <s_bill36_at_yahoo.co.uk> wrote:

> Dear AMBER
> I am going to do MM-PBSA calculation, in this caluclation I need to creat
> prmtop files for protein, ligand and protein-ligand.
> I was wondering about my protein, my protein PDB file has some crystallic
> water molecules, should I delete these water molecules when I creat my
> protein prmtop file in gas phase?
> Also, in tutorial no A3, you defined the following values:
> SURFTEN 0.0072
> SURFOFF 0.00
>
> from where did you get these values? according to the manual these values
> should be:
> SURFTEN 0.00542
> SURFOFF 0.92
>
> are they equal in the meaning, or what?
> Thanks in advance;
> Sincerely;
> S. Bill
>
>
>
>
>
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