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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>>
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Received on Wed Aug 30 2017 - 03:00:05 PDT
