Hi,
I can confirm that there appears to be a bug in version 13 that is not
present in 12 that prevents cpptraj from determining the correct number of
frames in a compressed trajectory. I am still testing to be sure, but this
may only be an issue with large compressed trajectories. While this does
not affect reading frames in cpptraj (i.e. actions in cpptraj itself will
work fine), it does cause problems for MMPBSA since version 13 cpptraj
isn't reporting the number of frames for these compressed trajectories. I
am currently working on a fix. Thanks for the report.
-Dan
On Tue, Mar 11, 2014 at 10:07 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Do the compressed trajectories actually contain 500 frames? That is to
> say, if you unzip one of the trajectories and load it into cpptraj (or even
> ptraj) does it still say 500 frames?
>
> Thanks,
>
> -Dan
>
>
> On Tue, Mar 11, 2014 at 2:14 PM, Ahmed Ayoub <atayoub.ualberta.ca> wrote:
>
>> Hi Daniel,
>>
>> Here is the input and output of the old cpptraj version. It is worth
>> mentioning that the trajectories were generated using Amber 12.18 GPU cuda
>> version.
>>
>> *input:*
>>
>>
>>
>>
>> *trajin ../Mprod6.mdcrd.gz 1 100000 4trajin ../Mprod7.mdcrd.gz 1 100000
>> 4trajin ../Mprod8.mdcrd.gz 1 100000 4trajin ../Mprod9.mdcrd.gz 1 100000
>> 4trajout prod6-9.nc <http://prod6-9.nc> netcdf*
>>
>> *output (old version):*
>>
>>
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>>
>> *CPPTRAJ: Trajectory Analysis. V12.4 ___ ___ ___ ___ | \/ | \/ |
>> \/ | _|_/\_|_/\_|_/\_|_INPUT: Reading Input from file traj.in
>> <http://traj.in> [trajin ../Mprod6.mdcrd.gz 1 100000 4]
>> [Mprod6.mdcrd.gz] contains 500 frames. Warning: Mprod6.mdcrd.gz stop
>> 100000 >= #Frames (500), setting to max. [trajin ../Mprod7.mdcrd.gz 1
>> 100000 4] [Mprod7.mdcrd.gz] contains 500 frames. Warning:
>> Mprod7.mdcrd.gz stop 100000 >= #Frames (500), setting to max. [trajin
>> ../Mprod8.mdcrd.gz 1 100000 4] [Mprod8.mdcrd.gz] contains 500
>> frames. Warning: Mprod8.mdcrd.gz stop 100000 >= #Frames (500), setting
>> to max. [trajin ../Mprod9.mdcrd.gz 1 100000 4] [Mprod9.mdcrd.gz]
>> contains 500 frames. Warning: Mprod9.mdcrd.gz stop 100000 >= #Frames
>> (500), setting to max. [trajout prod6-9.nc <http://prod6-9.nc>
>> netcdf]INPUT TRAJECTORIES: [Mprod6.mdcrd.gz] is an AMBER trajectory, Parm
>> 0 (with box info) (reading 125 of 500) [Mprod7.mdcrd.gz] is an AMBER
>> trajectory, Parm 0 (with box info) (reading 125 of 500) [Mprod8.mdcrd.gz]
>> is an AMBER trajectory, Parm 0 (with box info) (reading 125 of 500)
>> [Mprod9.mdcrd.gz] is an AMBER trajectory, Parm 0 (with box info) (reading
>> 125 of 500) Coordinate processing will occur on 500 frames.PARAMETER
>> FILES: 0: ../com-wat.top, 379197 atoms, 119489 res, ortho. box, 117759
>> mol,
>> 117250 solvent mol, 500 framesREFERENCE COORDS: No reference coordinates.
>> No frames defined.OUTPUT TRAJECTORIES: [prod6-9.nc <http://prod6-9.nc>]
>> is
>> a NetCDF AMBER trajectory, Parm 0: Writing 500 framesACTIONS: Initializing
>> 0 actions:BEGIN TRAJECTORY
>> PROCESSING:.....................................................PARM
>> [com-wat.top]: Setting up 0 actions.----- [Mprod6.mdcrd.gz] (1-497, 4)
>> -----*
>> * 0% ....etc*
>>
>>
>> *Output (New version):*
>>
>>
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>> *CPPTRAJ: Trajectory Analysis. V13.22 ___ ___ ___ ___ | \/ | \/
>> |
>> \/ | _|_/\_|_/\_|_/\_|_ AmberParm Title: [default_name]
>> Radius Set: H(N)-modified Bondi radii (mbondi2)INPUT: Reading Input from
>> file traj_new.in <http://traj_new.in> [trajin ../Mprod6.mdcrd.gz 1
>> 100000
>> 4]Warning: Mprod6.mdcrd.gz: Number of frames in compressed traj could not
>> be determined. Frames will be read until EOF.
>> [Mprod6.mdcrd.gz] contains an unknown number of frames. [trajin
>> ../Mprod7.mdcrd.gz 1 100000 4]Warning: Mprod7.mdcrd.gz: Number of frames
>> in
>> compressed traj could not be determined. Frames will be read until
>> EOF. [Mprod7.mdcrd.gz] contains an unknown number of frames.
>> [trajin ../Mprod8.mdcrd.gz 1 100000 4]Warning: Mprod8.mdcrd.gz: Number of
>> frames in compressed traj could not be determined. Frames will be
>> read until EOF. [Mprod8.mdcrd.gz] contains an unknown number of
>> frames. [trajin ../Mprod9.mdcrd.gz 1 100000 4]Warning: Mprod9.mdcrd.gz:
>> Number of frames in compressed traj could not be determined.
>> Frames
>> will be read until EOF. [Mprod9.mdcrd.gz] contains an unknown
>> number
>> of frames. [trajout prod6-9_new.nc <http://prod6-9_new.nc>
>> netcdf]PARAMETER FILES: 0: com-wat.top, 379197 atoms, 119489 res, box:
>> Orthogonal, 117759 mol, 117250 solvent, 100000 framesINPUT TRAJECTORIES:
>> 0:
>> [Mprod6.mdcrd.gz] is an AMBER trajectory, Parm com-wat.top (Orthogonal
>> box)
>> (reading 25000) 1: [Mprod7.mdcrd.gz] is an AMBER trajectory, Parm
>> com-wat.top (Orthogonal box) (reading 25000) 2: [Mprod8.mdcrd.gz] is an
>> AMBER trajectory, Parm com-wat.top (Orthogonal box) (reading 25000) 3:
>> [Mprod9.mdcrd.gz] is an AMBER trajectory, Parm com-wat.top (Orthogonal
>> box)
>> (reading 25000) Coordinate processing will occur on 100000
>> frames.REFERENCE COORDS: No frames defined.OUTPUT TRAJECTORIES:
>> [prod6-9_new.nc <http://prod6-9_new.nc>] is a NetCDF AMBER trajectory,
>> Parm
>> com-wat.top: Writing 100000 frames (1-Last, 1)BEGIN TRAJECTORY
>> PROCESSING:----- [Mprod6.mdcrd.gz] (1-99997, 4) -----*
>> * 0% .....etc*
>>
>>
>>
>> Message: 1
>> Date: Fri, 7 Mar 2014 13:02:04 -0700
>> From: Daniel Roe <daniel.r.roe.gmail.com>
>> Subject: Re: [AMBER] MMPBSA TrajError
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAAC0qOa-Ooo5LDeiN3kMSgO2K+_
>> Hv7CALXYU_t=fvcBA_WwLCA.mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Hi,
>>
>> On Fri, Mar 7, 2014 at 12:32 PM, Ahmed Ayoub <atayoub.ualberta.ca> wrote:
>>
>> > and the MMPBSA.py I'm using is a relatively new one. I made sure of that
>> by
>> > running cpptraj from the new AmberTools build and it was unable to read
>> the
>> > number of frames.
>> >
>>
>> This is odd, there should be no version incompatibilities with trajectory
>> formats for any version of cpptraj since the trajectory formats have not
>> changed. Can you give me the exact cpptraj input and output for the old
>> and
>> new versions?
>>
>> -Dan
>>
>>
>> > The workaround was to save the coordinates once more using the new build
>> > cpptraj so that it can be understood by the new MMPBSA.py.
>> >
>> > Thanks for your help.
>> >
>> > Ahmed Ayoub
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Mar 11 2014 - 22:00:03 PDT
