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
