AMBER Archive (2009)

Subject: [AMBER] Computational Alanine Scanning using mm_pbsa, any tutorial for amber9 or amber 10 version?

From: Haizhen Zhong (hzhong_at_mail.unomaha.edu)
Date: Fri Jun 05 2009 - 18:17:01 CDT

   Dear AMBER users,
   The ambermd.org website only provide using mmpbsa wild-type protein-ligand delta G.
   Is there any tu AMBER9?
   I have a copy of mmpbsa.perl from amber 6, I refer to the mm_pbsa.p amber9 version, and added mutation information in the regular @MAKECRD section in the extract_coords.mmpbsa file for amber9, according to the o nline tutorial, please see below,
   #
   BOX NTOTAL &nb NSTART &n NSTOP &nb NFREQ & NUMBER_MUTANT_GROUPS 1
   MUTANT_ MUTANT_ATOM2 MUTANT_KEEP &n MUTANT_REFERENCE&nb NUMBER_LIG_GROUPS &nb LSTART LSTOP & L LSTOP NUMBER_RE RSTART RSTOP&nb then, perl ./mm_pbsa.pl extract_coords.m it says,
   "Can't use string ("578") /opt/scripps/amber9//src/mm It seems it does not extract_coord file. Can reply and help out?
   Than Andy
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