AMBER Archive (2004)

Subject: Re: AMBER: tmd questions

From: Viktor Hornak (hornak_at_csb.sunysb.edu)
Date: Thu May 13 2004 - 07:16:36 CDT


Yes, that's the easiest way to do it. Experimenting with buffer width in
solvatebox will get you pretty close to having roughly the same number
of waters. Covert the system with bigger number of waters to pdb using
"ambpdb", delete superfluous waters in pdb and read it back into leap. I
think you also need to tell leap that it's a periodic system (e.g.
setbox mymol vdw 1.0) - it doesn't know that the pdb file with waters in
is supposed to be a periodic system.

Cheers,
-Viktor

Carlos Simmerling wrote:

>perhaps you can save as PDB file and delete
>the extra waters from 1, then reload it into
>leap. I haven't done that myself, though.
>
>----- Original Message -----
>From: "hj zou" <hjzou_at_iris3.simm.ac.cn>
>To: <amber_at_scripps.edu>
>Sent: Wednesday, May 12, 2004 10:00 PM
>Subject: AMBER: tmd questions
>
>
>
>>Dear amber usersúČ
>> I wanna perform a TMD simulatin in amber 7.The initial and target
>>
>structures of protein are ready.But when I try to add waters by using
>solvatebox,they have quite different numbers of waters in total which will
>produce "inconsistent numbers...." error message while running TMD.So, how
>can add same number of waters to both initial and target proteins?
>
>> Any suggestions are highly appreciated.
>> best regards
>>
>>
>>
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