Dear all,
I tried to image with ptraj (amber9) the trajectory of a long MD
simulation of a protein with its ligand and a peptide. I managed finally
to have all molecules in the same box, but the ligand and the peptide
jump often inside the same box a few Angstrom back and forth, so that
they even overlap !!! with the protein. So there is definitely something
going completely wrong. Below is the ptraj-file. As I have already
struggled with this problem for weeks I would be very grateful for any
suggestion.
Thank's a lot, Nadine
------------------------------
trajin all_trajectories.x.gz 1 -1 1
strip :WAT,Na+,Cl-
center :1-271 mass origin #protein
image origin center
center :1-271,288 mass origin #protein+L
image origin center
center :1-288 mass origin #protein+peptide+L
image origin center
trajout *.dry.c.binpos binpos
go
------------------------------------------------------------
Dr. Nadine Utz
Molecular Modelling & Bioinformatics Group
Institute for Research in Biomedicine (IRB) Barcelona
Parc Científic
c/ Baldiri Reixac 10
08028 Barcelona
SPAIN
phone: +34 934 039 073
http://mmb.pcb.ub.es
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Received on Mon Sep 13 2010 - 07:30:04 PDT
