AMBER Archive (2008)

Subject: Re: Re: AMBER: Combine mdcrd

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Fri Jan 04 2008 - 15:26:32 CST

File prmtop before embedding the protein complex into the membrane, and water
solvate, does contain a single WAT, listed as the last residue, after the
protein residues and the ligand. It must be for the crystallization water that
was left in place.
 
Using the ptraj script:

trajin prod1.mdcrd.gz
trajin prod2.mdcrd.gz
trajin prod3.mdcrd.gz
trajout prod1-3_no_wat_pop_nobox.mdcrd nobox
strip :WAT
strip :POP

and the above prmtop, deprived of that single WAT, the protein complex comes
out cleanly.

You were absolutely right, WAT was not in the mdcrd file.

Thanks a lot
francesco

--- Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:

> it's not clear why it isn't removed if the name is really WAT and
> you told ptraj to strip :WAT
> perhaps it is not really in the traj file but only in your prmtop?
> did you try a prmtop with no WAT at all (and specifying nobox in the
> trajout)?
>
>
> On Jan 4, 2008 12:36 PM, Francesco Pietra <chiendarret_at_yahoo.com> wrote:
>
> > very sorry. I reported mistakenly. Using the combined mdcrd with prmtop
> > before
> > embedding the complex into the membrane and solvating, the anomaly is not
> > at
> > the protein. It is for a water molecule not stripped. The two hydrogens
> > are at
> > the periphery of the protein, and the oxygen atom is far away from the
> > protein
> > complex. Requesting in Chimera color by element for the selected WAT, this
> > is
> > quite clear. Is it possible to remove this water molecule from the
> > combined
> > mdcrd file without passing through a pdb?
> > francesco
> >
> > --- Francesco Pietra <chiendarret_at_yahoo.com> wrote:
> >
> > > Date: Fri, 4 Jan 2008 09:23:45 -0800 (PST)
> > > From: Francesco Pietra <chiendarret_at_yahoo.com>
> > > Subject: Fwd: Re: AMBER: Combine mdcrd
> > > To: Amber <amber_at_scripps.edu>
> > >
> > > I forgot to add that I also had tried the combined mdcrd with prmtop
> > before
> > > embedding the protein complex into POPC and water solvating. When both
> > WAT
> > > and
> > > POP are stripped, the structure is only partially distorted (the
> > protein, not
> > > its complex). When only WAT is stripped, a chaotic structure is seen.
> > Perhaps
> > > some problems arise from having docked with a water molecule at the
> > filter,
> > > which is removed when I do the stripping.
> > >
> > > francesco
> > >
> > >
> > > --- Francesco Pietra <chiendarret_at_yahoo.com> wrote:
> > >
> > > > Date: Fri, 4 Jan 2008 09:07:15 -0800 (PST)
> > > > From: Francesco Pietra <chiendarret_at_yahoo.com>
> > > > Subject: Re: AMBER: Combine mdcrd
> > > > To: amber_at_scripps.edu
> > > >
> > > >
> > > > --- Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
> > > >
> > > > > once you produce the stripped traj file you will need a prmtop to
> > match
> > > > > it.
> > > >
> > > > I suspected (as I wrote) that this was needed, though I did not know
> > how to
> > > > get
> > > > prmtop for the combined, stripped trajectory. Notice that - the way I
> > > carried
> > > > out the process - "strip :WAT" did not remove all water molecules. A
> > > > peripheral
> > > > portion of them is still seen in Chimera.
> > > >
> > > >
> > > > >it isn't clear what you mean by "weird structures". are you using
> > the
> > > > > prmtop with water and pop to view the traj that does not have them?
> > > > >
> > > > > On Jan 4, 2008 11:37 AM, Francesco Pietra <chiendarret_at_yahoo.com>
> > wrote:
> > > > >
> > > > > > I am getting weird structures by combining mdcrd with either one
> > > > > > combine_mdcrd.ptraj:
> > > > > >
> > > > > >
> > > > > > trajin prod1.mdcrd.gz
> > > > > > trajin prod2.mdcrd.gz
> > > > > > trajin prod3.mdcrd.gz
> > > > > > trajout prod1-3_no_wat_pop.mdcrd
> > > > > > strip :WAT
> > > > > > strip :POP
> > > > > >
> > > > > >
> > > > > > trajin prod1.mdcrd.gz
> > > > > > trajin prod2.mdcrd.gz
> > > > > > trajin prod3.mdcrd.gz
> > > > > > trajout prod1-3_no_wat.mdcrd
> > > > > > strip :WAT
> > > > > >
> > > > > > Then:
> > > > > >
> > > > > > ptraj my.prmtop < combine_mdcrd.ptraj
> > > > > >
> > > > > > where my.prmtop is the one for the original trajectories to
> > combine.
> > > > > >
> > > > > > It deals of a protein complex in a POPC membrane, all in a water
> > box.
> > > > Even
> > > > > > the
> > > > > > structure of the non-polymeric ligand is completely disordered. Of
> > > > course,
> > > > > > each
> > > > > > trajectory to combine is OK. If anything, prod1 was obtained with
> > > > > 0.002fstime
> > > > > > step, the other two with 0.0015fs timestep.
> > > > > >
> > > > > > Should prmtop be regenerated (how?) to get all fitting? My final
> > aim is
> > > > to
> > > > > > carry out a cluster analysis.
> > > > > >
> > > > > > Additionally, once the above is set in order, it is not clear to
> > me how
> > > > to
> > > > > > add
> > > > > > to the ptraj script the request for rmsd for both the protein and
> > the
> > > > > > ligand.
> > > > > >
> > > > > > Thanks
> > > > > > francesco pietra
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> >
>
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> > > > > ===================================================================
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> --
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> CMM Bldg, Room G80
> Stony Brook University E-mail: carlos.simmerling_at_gmail.com
> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
> ===================================================================
>

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