Thanks Jason,
It actually worked. I was exactly doing the same mistake and was manually
editing pdb file.
Thanks for your response.
Regards,
Hirdesh
On Sat, Jan 14, 2012 at 8:07 PM, Jason Swails <jason.swails.gmail.com>wrote:
> I am guessing that you are stripping the PDB by hand, correct? If so, I'm
> guessing that the stripping you're doing by hand is __not__ the same as the
> stripping being done by ptraj. If they were the same this would not be
> happening.
>
> What I would suggest is using ptraj to generate the PDB file instead using
> this file:
>
> trajin prod.mdcrd 1 1 1
> trajout stripped_pdb.pdb
> strip :WAT
> strip :Cl-
>
> This should give you a compatible PDB file (which will give you a
> compatible prmtop when run through leap).
>
> As a side note, you can combine your two strip commands into
>
> strip :WAT,Cl-
>
> if you wanted to.
>
> HTH,
> Jason
>
> On Sat, Jan 14, 2012 at 9:27 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com
> >wrote:
>
> > Hi All,
> > I am trying to reduce my trajectory size so that I can visualize the same
> > using VMD. I tried following steps:
> >
> > 1) Striping of water from trajectories
> >
> > trajin prod.mdcrd 1 500 1
> > trajout traj_no_wat.mdcrd mdcrd
> > strip :WAT
> > strip :Cl-
> >
> > 2) New Topology File generation:
> > .rst file from production run --> use of ambpdb command to generate the
> pdb
> > file --> striping of water and ions from the generated pdb file
> > (protein-ligand complex only)
> >
> > 3) use of tleap to generate new topology ( prod_nowat.prmtop) file for
> the
> > ion and water stripped complex. The new files are successfully geneated
> > without any error.
> >
> > Now I am trying to visualize the no_wat.mdcrd and prod_nowat.prmtop in
> VMD.
> > I am getting unusual bonds in the structures. Please suggest me the
> > correction required??
> >
> > Thanks
> >
> > Hirdesh
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Jan 15 2012 - 21:00:02 PST
