AMBER Archive (2008)

Subject: Re: AMBER: Combine mdcrd

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Fri Jan 04 2008 - 11:07:15 CST

--- 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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