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)
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Received on Tue Mar 11 2014 - 13:30:03 PDT
