Hi Yip,
This one: http://ambermd.org/doc12/AmberTools13.pdf
Pawel
On 02/05/2014 11:23 PM, Yip Yew Mun wrote:
> 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 - 21:00:03 PST
