Thanks for reply.
Here I have tried as you have suggested.
When check number of water using watershell command for lower 3 angostrom approx
4-5 water molecule and for upper 5 angostrom approx 6 - 10 water through the
trajectry.
But when I used closest command water which it is selecting are too far from mask.
I was gussing that this is because of since it was firt 2ns run trajectry after
total 1ns heating and
equilibration steps but if watershell command showing that water availabel at
3 angostrom distace from mask.Then why not closest command showing this?
> 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
>>>
>>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 16 2011 - 11:30:04 PDT
