[gmx-users] Fwd: i want to use water_detetor.pl script

[Mahboobe Sadr]

I tried this script with ref atom O11 and also with N4 of DPPC, but it
cleaned waters between leaflets and also waters below the bottom leaflet,
what's the wrong?

Best Regards

M.Sadr



On Wed, Jun 24, 2015 at 5:06 PM, A. mohammadzadeh <
a.mohammadzadeh92b at gmail.com> wrote:

>
>
> On Sun, Jun 14, 2015 at 5:24 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 6/14/15 2:37 AM, A. mohammadzadeh wrote:
>>
>>> Hello dear users
>>>
>>> i want to  use  water_deletor.pl script to delete waters that has
>>> penetrated in lipid bilayer.How do i choose atom reference?
>>>
>>>
>> It depends on what your lipid is, and the choice is somewhat empirical.
>> Hydration typically exists into the glycerol region, so waters deeper in
>> the hydrophobic core should be deleted.  See usage info in the header of
>> the script itself for an example for DPPC.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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>
>