From: Robert Duke <>
Date: Tue, 6 Apr 2010 09:20:50 -0400

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
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.*

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Received on Tue Apr 06 2010 - 06:30:03 PDT
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