AMBER Archive (2009)

Subject: Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why?

From: case (case_at_biomaps.rutgers.edu)
Date: Mon Aug 17 2009 - 21:56:17 CDT

On Mon, Aug 17, 2009, Catein Catherine wrote:
>
> I see. Thank you very much for your help. Are there anything to do
> with how I prepare the snapshot? It seems to me that I should strip all
> the water from the mdcrd files before doing MM-GBSA analysis. If it is
> the case, how can I do it?

This is correct: the whole idea behind MM-PBSA or MM-GBSA is to not have
explicit waters. The "strip" command in ptraj can help you do this.

...dac

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