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.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.
>
> ...dac
>
>
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--
Ashish Runthala,
Faculty Division III,
Assistant Lecturer, Biological Sciences,
Birla Institute of Technology and Science,
Pilani, Rajasthan- 333031
INDIA
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Received on Wed Aug 19 2009 - 23:22:26 PDT
