AMBER Archive (2009)

Subject: Re: [AMBER] How to strip water for MM/GBSA calculations?

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Aug 21 2009 - 05:53:59 CDT

it is not necessary, but typical. your script looks fine. make sure that you
create a prmtop fil without water that matches the strip.mdcrd.

2009/8/21 Catein Catherine <askamber23_at_hotmail.com>

>
> Dear All,
>
>
>
> Could you mind to let me know if it is necessary to strip water from the
> mdcrd files before extracting snapshot for MM/GBSA calculation? If yes,
> could you mind to let me know if it is the correct ptraj file to be use?
>
>
>
> > trajin xxx.mdcrd
> >
> > trajout xxx_strip.mdcrd
> >
> > strip :WAT
>
>
>
> Best regards & many thanks in advanced,
>
>
>
> Cat
>
>
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