AMBER Archive (2008)

Subject: Re: Re: AMBER: Combine mdcrd

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Jan 04 2008 - 11:30:31 CST

make sure that you're treating the box info properly-
without specifying "nobox", the stripped traj will still have box info
and you may have to tell the viz program that.

On Jan 4, 2008 12:23 PM, Francesco Pietra <chiendarret_at_yahoo.com> wrote:

> 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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