Yep, you are right.
This term is related to packing of the water. The value > 2.0 produces
large emptiness cavities between water layer and membrane which seems
not good..
2017-08-30 11:43 GMT+02:00 Bill Ross <ross.cgl.ucsf.edu>:
> Also, you can experiment interactively in xleap til you figure out what
> works, then use it in tleap for production. You just want to see water
> placement quickly before trying another permutation.
>
>
> On 8/30/17 2:39 AM, James Starlight wrote:
>> I need it to make in tleap because it is a part of some script for
>> automatic GPCR preparation. After tleap I post-process the system with
>> some python script which cut the water licked into the membrane during
>> to solvation - it is not a problem.
>> Thus, initially I need to add correct number of waters above the
>> lipid leaflets of the system (along Z) with receptor and lipids only.
>> I don't understand what is 1.5 number in
>> solvatebox protein TIP3PBOX { 0.0 0.0 15 } 1.5
>>
>> 2017-08-30 11:30 GMT+02:00 Bill Ross <ross.cgl.ucsf.edu>:
>>> Experiment - 'edit mymol' in xleap will make it go fast.
>>>
>>> Bill
>>>
>>>
>>> On 8/30/17 2:25 AM, James Starlight wrote:
>>>> Dear amber users!
>>>>
>>>> I am using tleap to generate water box for the GPCR protein embedded
>>>> within the 120 lipids.
>>>>
>>>> solvatebox protein TIP3PBOX { 0.0 0.0 15 } 1.5
>>>>
>>>> My question: what the params for solvatebox may be desirable to
>>>> generate a proper number of water along Z dimensions of the membrane?
>>>>
>>>> Thanks!
>>>>
>>>> James
>>>>
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Received on Wed Aug 30 2017 - 03:00:06 PDT
