[AMBER] minimization/equilibration amber 12 - wont generate .mdcrd and .ene files

From: Amparo Garcia Lopez <Amparo.GarciaLopez.unige.ch>
Date: Thu, 14 Nov 2013 12:16:19 +0000

Dear all,

we have been trying to run a minimization followed by equilibration in amber12. We have tried both pmend and sander, and with both we have the following problem.

We use these options

mpirun -np 4 $AMBERHOME/bin/sander.MPI -O -i md8.in -o md8.out -p md.top -c md7.crd -ref md7.crd -r md8.rst -x md8.mdrcd -e md8.ene &

the program will not generate the trajectory file (-x option) nor the energies file (-e option). However, the program does generate the .rst (-r) and .out (-o) files. We have tried with two different molecules, and the same thing happens, so it's not the system.

Any idea with sander/pmend won't recognise the -x and -e options?

Thank you very much in advance for your help.
Best wishes,

Amparo Garcia-Lopez, Ph.D.

Pharmaceutical Biochemistry
School of Pharmaceutical Sciences
University of Geneva
Quai Ernest-Ansermet 30
1211 Genève 4 - Switzerland

Tel: +41 (0)22 379 3376
Fax: +41 (0)22 379 3360

e-mail: Amparo.GarciaLopez.unige.ch
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Received on Thu Nov 14 2013 - 04:30:02 PST
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