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 - 03:04:08 CDT

Hi Francesco,

I am not absolutley sure, but I think ambpdb and ambmask are made for working with .restrt and/or .inpcrd files not with trajectories.

Whjat i wanted to suggest to use the trajout command in ptraj to create .pdb files where the water is stripped.

Just replace

trajout <directory>/ptraj.mdcrd trajectory

with

trajout <directory>/ptraj.pdb pdb

in the ptraj input file that you used fpr creating the stripped trajectory file.

gl Alexander 

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

--- Francesco Pietra <chiendarret_at_gmail.com> schrieb am Do, 12.6.2008:

> Von: Francesco Pietra <chiendarret_at_gmail.com>
> Betreff: Re: AMBER: Combine mdcrd while stripping WAT problem
> An: amber_at_scripps.edu
> Datum: Donnerstag, 12. Juni 2008, 9:09
> Hi:
> That is an excellent suggestion. Actually, I had already
> tried that,
> with both ambpdb and ambmask. Failure in both cases,
> however. I just
> describe here what happened with the first. Maybe someone
> is
> interested.
> 
> $AMBERHOME/exe/ambpdb -p complex_pop_box.prmtop <
> combined_production.mdcrd > combined_production.pdb
> 
> New format PARM file being parsed
> Version 1.000 Date 03/25/08
> forrtl: severe (64): input conversion error, unit -5, file
> Internal
> Formatted read
> 
> To rule out that it was a problem of shortage of memory, I
> run the
> same for one of the production chunks. Exactly the same
> error.
> 
> Also, I tried with an initial prmtop/inpcrd combination for
> both my
> ligand and the protein, and both ambpdb and ambmask worked
> correctly,
> also in Amber10. I assume that mdcrd should behave as
> inpcrd to this
> respect.
> 
> However, as the study at hand urged to be completed,
> yesterday evening
> I went to a debian linux machine with larger RAM. I
> installed VMD and
> could load all frames for the whole system of complex in
> hydrated
> membrane and box, performing clustering and getting fine
> RMSD vs time
> for both the protein and the ligand with plugins. Like I
> did months
> ago to circumvent a similar problem of getting matching
> prmtop/mdcrd.
> 
> That does not mean that I  am not interested in getting a
> workable
> prmtop for a combined mdcrd for my systems. Either I was
> not correctly
> doing (which is the most likely possibility), or a program
> to get
> matching prmtop/mdcrd would be most useful. I understand
> the problem
> of convention, however. In fact, for the initial
> preparation of my
> systems, the part taken by Chimera was most troublesome. I
> had to
> rearrange atom names with four characters - and much more,
> with great
> help by Eric and Elaine - in order that leap could
> understand them.
> 
> Thanks
> 
> francesco
> 
> On Thu, Jun 12, 2008 at 7:59 AM, Alexander Metz
> <alexander_metz2000_at_yahoo.de> wrote:
> > 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)
> >>
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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)
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
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