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?
Best regards,
Andrew
06.12.2009, 10:09, "Bill Ross" <ross.cgl.ucsf.edu>:
>>> šmaybe it s posible to strip waters from .rst file and then convert
>>> šit to PDB.
>> šIdeally someone (it could be you) would add a -nowat option to
>> šambpdb to do the right thing.
>
> PS - stripping from rst means you'd have to generate the no-wat
> prmtop for ambpdb to work with the modified rst. Making the change
> to ambpdb is more sensible I think. While at it, a -nosolvent flag
> could strip whatever prmtop thinks is solvent (there is a pointer
> to the solvent section as I remember), which might provide
> the convenience of leaving in xtal waters.
>
> Bill
>
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Received on Sun May 29 2011 - 11:00:02 PDT
