In order to use distance-based mask parsing in ptraj/cpptraj you need
to load a reference structure; the distance-based mask parser will use
that as a reference.
Also check out the 'watershell' and 'closest' commands for checking
solvent around a specific area.
-Dan
On Fri, Feb 8, 2013 at 4:06 PM, Do Yong Kim <kdy2002.gmail.com> wrote:
> Dan,
>
> I have tried your fix but still no water has been removed. strip
> !(:1-11<:5.0)
>
> I have tried other combinations but it did not work
>
> am I doing something wrong here?
>
> Kim
>
>
> 2013/2/7 Daniel Roe <daniel.r.roe.gmail.com>
>
>> Hi,
>>
>> On Thu, Feb 7, 2013 at 5:03 PM, Do Yong Kim <kdy2002.gmail.com> wrote:
>> > strip !(:1-11<5.0)
>>
>> This mask should be "!(:1-11<:5.0)".
>>
>> -Dan
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-9119 (Fax)
>>
>> _______________________________________________
>> 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
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 08 2013 - 15:30:03 PST
