AMBER Archive (2009)

Subject: [AMBER] Is it the correct procedures to strip water for MM/GBSA calculations?

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Tue Aug 18 2009 - 00:06:18 CDT

Dear Prof. Case,

 

Thank you. Could you please kindly tell me more about how can I do it properly? It is what I guess, but I dont' know if it is correct, pls kindly instruct.

 

(1) Get mdcrd files from explicit solvent simulations.

 

(2) Use ptraj with following command lines to generate water stripped mdcrd files for MM/GBSA calculations.

trajin xxx.mdcrd

trajout xxx_strip.mdcrd

strip :WAT

 

(3) as usual, readin the xxx_strip.mdcrd files for MM/GBSA analysis.

 

Is it correct or stupid things still appear in the procedures?

 

Best regards,

Cat

 

 

 
> Date: Mon, 17 Aug 2009 22:56:17 -0400
> From: case_at_biomaps.rutgers.edu
> To: amber_at_ambermd.org
> Subject: Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why?
>
> 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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