Dear Andrew,
> Dear Amber developers, are there any shifts in this question?
> I need to remove water from dataset of PDB files and it would be better to do this through modeification of the shell script just by adding -nowat flag to ambpdb rather than stripping water from prmtop, rst or mdcrd files.
> Maybe there are any scripts for this in the community now?
if I understood your problem correctly, your task should be easily
accomplished using Linux' command line grep:
ambpdb -p system_water.top < system_water.crd | grep -v WAT \
> system_naked.pdb
Of course, you could strip off ions as well.
Regards,
Anselm
Bioinformatik
Friedrich-Alexander-Universität Erlangen-Nürnberg
Germany
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Received on Sun May 29 2011 - 13:30:02 PDT
