Ok I have used the following command.
To process mdcrd file I have used
trajin 1sa3_mono_prod2.mdcrd 1 2000 1
closest 10 :115 first
trajout 1sa3_mono_prod2-close.mdcrd mdcrd
To generate new topology I have extracted one of the snapshort
trajin 1sa3_mono_prod2.mdcrd 1 2000 1600
trajout 1sa3_mono_prod2.rst restrt
Then convert above .rst file into PDB, modified that pdb file so it contains only
complex, ions and 10 water molecules and finaly used this pdb file generate new
prmtop in tleap.
> Hi,
>
> On Thu, Mar 3, 2011 at 12:00 PM, Sangita Kachhap <sangita.imtech.res.in> wrote:
>> Also generate new prmtop contain protein-DNA complex and 10 water.
>
> How did you generate your output trajectory and the new parmtop (exact
> commands)? The effect you're describing sounds like box information
> may be missing from your generated topology/coordinate files.
>
> -Dan
>
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Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Thu Mar 03 2011 - 20:00:03 PST
