AMBER Archive (2008)

Subject: Fwd: Re: AMBER: Combine mdcrd

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Fri Jan 04 2008 - 11:36:49 CST

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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> > >
> > >
> > >
> > > --
> > > ===================================================================
> > > 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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