Slight correction - watershell actually only counts the number of
solvent molecules within a certain distance from solute - it doesn't
actually modify the state. So if you want to keep solvent mols within
a certain distance from solute you would have to first run watershell
to get an idea for how many waters are in a given shell, then run a
'closest' command based on that number.
-Dan
On Wed, Mar 16, 2011 at 8:59 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> There is no distance cutoff - 'closest X <mask>' modifies the state so
> that only the X closest solvent molecules to atoms in <mask> are kept.
> If you want to keep solvent within a certain distance from solute see
> the 'watershell' command in the ptraj section of the ambertools
> manual.
>
> -Dan
>
> On Wed, Mar 16, 2011 at 6:07 AM, Sangita Kachhap <sangita.imtech.res.in> wrote:
>>
>> Hello al
>>
>> I have query regarding ptraj closest command, I want to know distance cutoff of
>> closest command.
>>
>>
>> With regard
>>
>> Sangita Kachhap
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Wed Mar 16 2011 - 06:30:02 PDT
