Hi, thanks for the prompt reply.! Which amber tools manual would it be?
Regards
Yip Yew Mun
Graduate, PhD
Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University
On 6 Feb, 2014, at 11:47 am, Pawel <pawelrc.gmail.com> wrote:
> Hi,
>
> You can also use the AddToBox program. See section 14.4.3 of the
> AmberTools manual.
>
> Pawel
>
>
>
> On 02/05/2014 10:29 PM, Jason Swails wrote:
>> On Wed, Feb 5, 2014 at 10:01 PM, Yip Yew Mun <yipy0005.gmail.com> wrote:
>>
>>> Hi, I wish to ask if it's possible to specify a fixed number of water
>>> molecules when solvating a protein molecule? Thanks.
>>>
>> I assume you mean in tleap. The answer is no -- this is not possible. The
>> best you can do is make your solvent buffer large enough so that you have
>> almost the exact number of water molecules you want (try to get as close to
>> your target value as possible). Then you can use ParmEd or cpptraj to
>> strip out the extra water molecules you don't want to reach your target
>> value.
>>
>> An alternative is to use packmol to build your system.
>>
>> HTH,
>> Jason
>>
>
>
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Received on Wed Feb 05 2014 - 20:30:02 PST
