Problems with long bonds have always turned out to be a discrepancy
in either atom numbers or box info between mdcrd and prmtop.
You could look at your 1sa3_mono_prod2-close.mdcrd file, taking
one frame and making sure there is no box info, counting the
numbers and dividing by 3 to find the number of atoms. In the
prmtop I believe the number of atoms is the first number, and
the ifbox parameter tells you if it has a box (see the parm
format on the amber web).
Bill
> 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 Fri Mar 04 2011 - 16:00:03 PST
