AMBER Archive (2008)

Subject: AMBER: alascan error

From: Larry Layne (
Date: Wed Dec 17 2008 - 14:19:22 CST

I am confused about the set-up for the alascan option of mm_pbsa. The settings in the sample file and the corresponding atoms don't seem to match up. I would assume between the MUTANT_KEEP (carbonyl carbon) and the MUTANT_REFERENCE (beta-carbon) there will always be a consistent number of atoms, but that is not what is being shown in the manual. The number seem more random than the actual scheme that is present. I have attempted to figure out what my problem is with my alascan definitions, but I can not find them. Any help or feedback would be greatly appreciated.


I've include a copy of my ligand file as well to show connectivity appears to be correct with regards to my alascan values.

---------------------------- Original Message ----------------------------
Subject: alascan MUTANT_KEEP error
From: "Larry Layne" <>
Date: Tue, December 16, 2008 2:07 pm

I am attempting to perform an alanine scan with a protein-protein interaction and I am getting an error that I don't understand. The error reported is "Something wrong with MUTANT_KEEP definitions". I have attached the log file. The residues to be mutated are DSLL, and that is the order they are drawn up in the input file. I looked in the archive for possible solutions, but the only possibility I saw was the need for topology files for each mutant. Is that necessary? And if so, where do I input the location of the mutant topology files in my input, since I don't see anything about this in the manual?

Also, in mutating the serine residue, there is not CG atom, so should I assume that I should put the OG atom for the MUTANT_ATOM1 variable?

Thanks for your time,

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