AMBER Archive (2003)

Subject: mm_pbsa and ALA scan

From: Ahammadunny Pathiaseril (ahamed_at_giti.ccrc.uga.edu)
Date: Wed Jan 29 2003 - 10:24:06 CST

Hi everyone,

          In mm_pbsa I do not understand how the the option, AS=1, works. This
is for the input which starts with @ALASCAN. I was under the impression that a
residue in a protein can be mutated to ALANINE and then the free energy
change associated with this mutation can be calculated. But the program does
not seem to work that way. When AS=1 and GC=1 are set with other options
like MM,GB, or MS, snapshots of the coordinates of the mutated protein are
written into separate files. But then it gives the error message:'mismatch
in the number of atoms between the coordinate and the topology files.' This
may be because of the fact that the topology file is for the wild type( before
the mutation) protein. So it requires a topology file for the mutant.

          Is a topolgy file needed for each mutant ?

                           or

          Is there another option to do this kind of calculation ?

         
          Sincerely yours,

         A. PATHIASERIL

         Complex Carbohydrate Research Center

         University of Georgia

         Athens, Georgia.