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 (ashish.runthala_at_gmail.com)
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<case_at_biomaps.rutgers.edu> 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.
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