Dear Amber users,
I would like to try different setups
for PB calculations. As I will be generating my Leap files
using different radii set (bondi, mbondi, mbondi2, mbondi3, Rmin,
Parse) for GB calculations,
it will as I assume affect my results evetually when I use them in PB calculations with different
INP = 1&2, RADIOPT=0&1 or I also want try hybrid models with
IVCAP=1&5...
Is it okay
to use default cavity_surften, cavity_offset for PB calculations
whenever I change the radii in xleap ?
I have prepared a small table for different setups where i change the INP, RADIOPT, IVCAP parameters by looking at the
AMBER 12 / Examples
/TEMPLATE_INPUT_SCRIPTS / SURFTEN_SURFOFF_Recommendations.pdf file
If anybody has experience about different radii effects on PB calculations and how we need to change the input, I will really appreciate if you can have a look at the table
and let me know if I need to change something in the procedure.
Best regards,
Berin Karaman
Medicinal Chemistry
Institute of Pharmacy
Martin-Luther-Universität Halle-Wittenberg
Wolfgang-Langenbeck-Str. 4
06120 Halle (Saale), Germany
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 01 2013 - 07:00:05 PDT
