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
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Jan 14 2012 - 07:00:03 PST
