Try 'help solvatebox' - I think it's a factor for packing. Packmol is
another prog people use for building boxes, may be more flexible.
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 - 03:00:04 PDT
