AMBER Archive (2009)

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

From: Ashish Runthala (
Date: Mon Aug 17 2009 - 22:02:43 CDT

Wow great it is ...i din't know about this strip command. So can i
remove TIP3P units from an explicitly solvated system and use some
other solvent system. Please guide me on this.

On Tue, Aug 18, 2009 at 8:26 AM, case<> wrote:
> 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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Ashish Runthala,
Faculty Division III,
Assistant Lecturer, Biological Sciences,
Birla Institute of Technology and Science,
Pilani, Rajasthan- 333031

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