Re: [AMBER] Blowing array; too many frames!!

From: Sangita Kachhap <sangita.imtech.res.in>
Date: Fri, 4 Mar 2011 09:26:52 +0530 (IST)

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
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