From: Juan Carlos <juan.munioz.iiq.csic.es>
Date: Tue, 06 Apr 2010 09:35:40 +0200

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 - 01:00:03 PDT
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