Hi,
This bug should be fixed by AmberTools 13 update 24, now available. If you
get a chance to try out the patch please let me know if it fixes the
problem you were having. Thanks again for the report.
-Dan
On Tue, Mar 11, 2014 at 10:41 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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):*
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> *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):*
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> *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)
>
--
-------------------------
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 Thu Mar 13 2014 - 08:00:03 PDT
