did you try using ptraj to extract a frame as a restart format and
then ambpdb on that?
I don't think you can use ambpdb on the mdcrd file.
On Thu, Jun 12, 2008 at 3:09 AM, Francesco Pietra <chiendarret.gmail.com> wrote:
> 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.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.gmail.com> schrieb am Mi, 11.6.2008:
>>
>>> Von: Francesco Pietra <chiendarret.gmail.com>
>>> Betreff: Re: AMBER: Combine mdcrd while stripping WAT problem
>>> An: amber.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.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.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.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.gmail.com> wrote:
>>> >>>> On Sun, Jun 8, 2008 at 11:40 AM, Francesco
>>> Pietra <chiendarret.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.
>>> >>>>
>>> -----------------------------------------------------------------------
>>> >>>> The AMBER Mail Reflector
>>> >>>> To post, send mail to amber.scripps.edu
>>> >>>> To unsubscribe, send "unsubscribe
>>> amber" (in the *body* of the email)
>>> >>>> to majordomo.scripps.edu
>>> >>>>
>>> >>>
>>> >>>
>>> >>>
>>> >>> --
>>> >>>
>>> -----------------------------------------------------------------------
>>> >>> The AMBER Mail Reflector
>>> >>> To post, send mail to amber.scripps.edu
>>> >>> To unsubscribe, send "unsubscribe
>>> amber" (in the *body* of the email)
>>> >>> to majordomo.scripps.edu
>>> >>>
>>> >>
>>> >>
>>> >>
>>> >> --
>>> >> 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.scripps.edu
>>> >> To unsubscribe, send "unsubscribe amber"
>>> (in the *body* of the email)
>>> >> to majordomo.scripps.edu
>>> >>
>>> >
>>> -----------------------------------------------------------------------
>>> > The AMBER Mail Reflector
>>> > To post, send mail to amber.scripps.edu
>>> > To unsubscribe, send "unsubscribe amber" (in
>>> the *body* of the email)
>>> > to majordomo.scripps.edu
>>> >
>>>
>>>
>>>
>>> --
>>> 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.scripps.edu
>>> To unsubscribe, send "unsubscribe amber" (in the
>>> *body* of the email)
>>> to majordomo.scripps.edu
>>
>>
>> __________________________________________________________
>> Gesendet von Yahoo! Mail.
>> Dem pfiffigeren Posteingang.
>> http://de.overview.mail.yahoo.com
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber.scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo.scripps.edu
>>
>
>
>
> --
> 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.scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Sun Jun 15 2008 - 06:07:28 PDT
