From: Daniel Roe <>
Date: Tue, 6 Apr 2010 12:25:53 -0400

Hi Juan,

Sander and PMEMD trajectories should be identical. The fact that ptraj was
able to read several sets before giving you the error indicates either the
trajectory is truncated/corrupted as Bob suggests, or the topology file you
are using doesn't match the one used to generate the trajectory. One way to
check if your trajectory is truncated is to calculate your expected number
of lines for each frame in the trajectory file:

#Lines = (#atoms * 3) / 10

Round up to the nearest integer if there is *any* remainder to the division,
and add 1 more if you have box coordinates (which appears to be the case).
So for example, a system with 332 atoms and box coordinates would have 101
lines each frame. Then just multiply by your expected number of frames, and
see if that number matches the output of a 'wc -l' command. In my above
example if I had 100 frames in the trajectory I would expect the file to
have 10100 lines - any less and I know I've got a problem somewhere. Let me
know if I can be of further help.


PS - Unless you need to visualize the trajectories in a windows environment
I would encourage you to switch to NetCDF formatted trajectories (using
ioutfm=1). They take up less space and are faster to process!

On Tue, Apr 6, 2010 at 9:20 AM, Robert Duke <> wrote:

> Hello Juan,
> I am wondering if either you ran out of space on the disk, did some
> preprocessing of the coordinate file, had some differences in the runs, or
> possibly ran the trajectory so long without wrapping that there was overflow
> in one of the number representations in the output file (look for "*"
> character in output) (I generally see this in the restart file first,
> however). There is essentially no difference in pmemd trajectory file
> output and sander trajectory file output (I think that for one of them, a
> blank title line may actually have more blanks, but that is it, and it does
> not matter at all). Over the course of a month I probably use ptraj to
> process microseconds worth of data from pmemd...
> Please first make sure that the file did not somehow get truncated on disk
> or otherwise corrupted; pmemd works fine for producing usable trajectories;
> otherwise folks would not have been using it for about 7 years :-) Someone
> more familiar with ptraj reading error situations may want to also
> comment...
> Regards - Bob Duke
> ----- Original Message ----- From: "Juan Carlos" <>
> To: <>
> Sent: Tuesday, April 06, 2010 3:35 AM
> Dear amber users,
> Iīm using Amber9. I run 2 dynamic simulations for the same molecule,
> explicit solvent and the same conditions. The only
> difference between them is that one is run with Sander.MPI and the other
> one with PMEMD. The problem appears when
> using ptraj to calculate the dihedrals; when processing the trayectory
> coordinates file from the Sander.MPI simulation, there
> is no problem with ptraj performance. However, when doing the same with
> the trayectory coordinates file of the PMEMD
> dynamic, I get the following error :
> /Processing Amber trayectory file Tri.coord
> Set 1 ........................................
> WARNING in read AmberTrayectory ( ) : fsetpos ( ) failed on when
> looking for box coordinates!
> /My ptraj command is as follows :
> ptraj Tri1A_1c4_water.tpp << EOF
> trajin Tri1A_1c4_water_equil_md.coord
> dihedral phi1 .63 .62 .61 .53 out phiSGX-IDS
> dihedral psi1 .62 .61 .53 .54 out psiSGX-IDS
> dihedral phi2 .41 .40 .39 .26 out phiIDS-SGN
> dihedral psi2 .40 .39 .26 .27 out psiIDS-SGN
> trajout dihedral.traj
> Both dynamics are run with the same topology and coordinates files, so I
> wonder if itīs maybe a problem of the format file PMEMD generates.
> Please, could anybode give me a hand? PMEMD is performing great with my
> system, but if I canīt process my output files
> itīs useless.
> Iīd be very please for your help.
> Thank your very much.
> *Juan Carlos Muņoz García.
> Institute of Chemical Research, Sevilla, Spain.
> Spanish Research Council.*
> _______________________________________________
> AMBER mailing list
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ   08854
AMBER mailing list
Received on Tue Apr 06 2010 - 09:30:02 PDT
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