Dear amber users:
I am calculating a protein-ligand complex in explicit water with the
goal to analyze the first solvents shells. To get all molecules back
into the original unit cell, I use the image command in ptraj. But since
the complex is moving in time, it is not in one cell, so that parts of
the molecule are not surrounded by solvents (I know that there are
images of the solvents molecules there. But these have to be generated
by translation of the unit cell, which is not easy to do for an external
program). Is there a possibility in ptraj or any other program to center
the unit cell on a specific atom or molecule. Then I could center it on
the protein and all molecules should then end up in only one cell.
Thank you very much for your help.
Thomas
--
________________________________________________________________________________
Dr. Thomas E. Exner
Juniorprofessur "Theoretische Chemische Dynamik"
Fachbereich Chemie
Universität Konstanz
78457 Konstanz
Tel.: +49-(0)7531-882015
Fax: +49-(0)7531-883587
Email: thomas.exner.uni-konstanz.de
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Received on Tue Aug 03 2010 - 04:30:03 PDT
