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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>
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Received on Wed Aug 30 2017 - 03:00:03 PDT
