AMBER Archive (2008)

Subject: Re: AMBER: Combine mdcrd while stripping WAT problem

From: Alexander Metz (alexander_metz2000_at_yahoo.de)
Date: Thu Jun 12 2008 - 00:59:18 CDT

Maybe you could create a working .prmtop file by:

(1) creating a .pdb file with trajout and then
(2) creating a new .prmtop file from this .pdb file using LEaP

Good luck,

Alexander 

-- 
++++++++++++++++++++++++++++++++++++++++++++++++++

--- Francesco Pietra <chiendarret_at_gmail.com> schrieb am Mi, 11.6.2008:

> Von: Francesco Pietra <chiendarret_at_gmail.com>
> Betreff: Re: AMBER: Combine mdcrd while stripping WAT problem
> An: amber_at_scripps.edu
> Datum: Mittwoch, 11. Juni 2008, 16:57
> Hi:
> Still unsuccessful in loading cleanly the combined
> (stripped) mdcrd
> files to VMD.
> Described here is what I did, should someone be so patient
> to check
> for mistakes.
> 
> I have a number of prmtop files, corresponding to the
> various steps. I
> have now tried the two most naked ones, from docking the
> ligand onto
> the protein with DOCK6.2. Here, a prmtop was for flex
> scoring, the
> other one from amber score in implicit medium, that is, WAT
> only
> appears in the prmtop as the last residue after all protein
> residues.
> I deleted WAT from either one of these two prmtop files and
> tried with
> VMD with the combined mdcrd, stripped of :WAT :POP, and
> nobox. Result:
> highly distorted protein and ligand at each snapshot.
> 
> Surely there are other combinations of mdcrd/prmtop. Those
> I tried
> (all other prmtop files - from embedding into the lipidic
> membrane -
> contain WAT BOX and result from 'solvate box model#
> TIP3Box 12.0') led
> to similarly distorted snapshots. I assume that I missed
> the right
> choice of combinations. Before trying other ones, it would
> help to
> appreciate where the above procedure is in error.
> 
> Thanks a lot
> francesco pietra
> 
> On Tue, Jun 10, 2008 at 10:03 AM, Carlos Simmerling
> <carlos.simmerling_at_gmail.com> wrote:
> > whether you say nobox depends on whether your new
> > stripped prmtop (and you must make one) has a box or
> > not. just be consistent and it should be ok.
> > distortions come from the mdcrd and prmtop not
> > have the same amount of data per frame, either
> > from mismatch in natom or mismatch in box presence.
> > calros
> >
> > On Tue, Jun 10, 2008 at 3:37 AM, Francesco Pietra
> <chiendarret_at_gmail.com> wrote:
> >> Hi:
> >> Perhaps you also refer to discussion I took part
> to last year for the
> >> same problem with Amber9.
> >>
> >> Like at that time, docking of the ligand was now
> carried out (DOCK6.2)
> >> with the protein embodying a single molecule of
> water of
> >> crystallization. That is, the prmtop corresponding
> to protein+ligand
> >> before embedding into the membrane contains that
> WAT. I already tried
> >> the WAT&POP stripped mdcrd with that prmtop.
> Did not work, i.e., both
> >> the protein and the ligand looked like heavily
> distorted at each
> >> snapshot when loading to VMD the stripped mdcrd
> file.
> >>
> >> I can try again with prmtop stripped (with text
> editor) of that WAT,
> >> although as carried out above it did not work.
> Before doing that, a
> >> question: is it meaningful to command
> 'nobox' while stripping only WAT
> >> (and not POP too)?
> >>
> >> Thanks for the suggestions.
> >> francesco pietra
> >>
> >> On Sun, Jun 8, 2008 at 9:33 PM, Carlos Simmerling
> >> <carlos.simmerling_at_gmail.com> wrote:
> >>> also, if you strip water, you might want to
> use the "nobox"
> >>> flag after trajout so that box coordinate are
> not written. by default
> >>> they are. if you use the correct prmtop
> corresponding to the
> >>> stripped system, try loading the trajectory in
> VMD using the
> >>> coordinates with box and see if it helps.
> there is lots of
> >>> discussion of this in the archives.
> >>>
> >>> On Sun, Jun 8, 2008 at 2:58 PM, Gustavo Seabra
> <gustavo.seabra_at_gmail.com> wrote:
> >>>> On Sun, Jun 8, 2008 at 11:40 AM, Francesco
> Pietra <chiendarret_at_gmail.com> wrote:
> >>>>> With Amber10, on accumulating ns of
> trajectory, I am facing a problem
> >>>>> of trajectory analysis unresolved
> since Amber9 for the same protein
> >>>>> and environment, though for a
> different ligand.
> >>>>>
> >>>>> The system is a large protein,
> carrying a large non-peptidic ligand.
> >>>>> It is embedded in a POP, TIP3P
> hydrated, membrane.  Everything flows
> >>>>> correctly, 39% faster with pmemd with
> respect to sander.MPI.
> >>>>>
> >>>>> What I am trying to do with ptraj is
> combining *.mdcrd while stripping WAT
> >>>>>
> >>>>> While a complete action would be:
> >>>>>
> >>>>> trajin prod1.mdcrd.gz
> >>>>> trajin prod2.mdcrd.gz
> >>>>> ......................
> >>>>> trajout prod1-#_no_wat.mdcrd nobox
> >>>>> strip :WAT
> >>>>> strip :POP
> >>>>>
> >>>>> I tried simply:
> >>>>>
> >>>>> trajin prod1.mdcrd.gz
> >>>>> trajin prod2.mdcrd.gz
> >>>>> ......................
> >>>>> trajout prod1-#_no_wat.mdcrd
> >>>>> strip :WAT
> >>>>>
> >>>>> That in view of using the *.prmtop for
> MD and in order not to change
> >>>>> the residue numbering.
> >>>>>
> >>>>> With the same *.prmtop  used for  MD,
> the combined file does not load
> >>>>> cleanly with VMD. As expected.
> >>>>
> >>>> What exaclty do you mean by "not load
> cleanly"? Do you get any error
> >>>> messages? Anyways, I'm not sure it
> could ever load correctly, since
> >>>> after stripping the waters the number of
> atoms in the prmtop file is
> >>>> different than in the prod1-#_no_wat.mdcrd
> file.
> >>>>
> >>>>> I removed all WAT from *.prmtop. The
> same problem.
> >>>>
> >>>> I suppose there's more to it than just
> removing the "WAT" residues.
> >>>> You may want to take a look into the
> 'rdparm' utility, described
> >>>> together with ptraj. (Check the
> "stripwater" and then "writeparm"
> >>>> commands).
> >>>>
> >>>> Gustavo.
> >>>>
> -----------------------------------------------------------------------
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> >>>
> >>>
> >>>
> >>> --
> >>>
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> >>
> >>
> >>
> >> --
> >> Dr Francesco Pietra
> >> Professor of Chemistry
> >> Accademia Lucchese di Scienze, Lettere e Arti,
> founded in 1594
> >> Palazzo Ducale
> >> 55100 Lucca (Italy)
> >>
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> 
> 
> 
> -- 
> Dr Francesco Pietra
> Professor of Chemistry
> Accademia Lucchese di Scienze, Lettere e Arti, founded in
> 1594
> Palazzo Ducale
> 55100 Lucca (Italy)
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the
> *body* of the email)
>       to majordomo_at_scripps.edu

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