AMBER Archive (2007)

Subject: AMBER: No radius found for K+ (MM_PBSA)

From: saurabh agrawal (imsam100_at_yahoo.co.in)
Date: Fri Dec 21 2007 - 08:45:01 CST

Dear Amber Users,

I am trying to calculate absolute free energy for the nucleotide molecule using MM_PBSA script of AMBER8. The system has some K+ ions in the active site. I wish to calculate the absolute free energy in presence of these ions.

Shall I include the radius in "mm_pbsa_calceneent.pm" file or any other file? If yes please let me know the accurate value of radius for K+ ion.

Shall I recompile the AMBER after addition of these values?

Any reply is of great help for me.

saurabh

 

       
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