Re: [AMBER] problem

From: Fernando Martín García <>
Date: Wed, 17 Jul 2013 14:54:57 +0200


Thank you, Jason That was the problem.

And also thanks for the
csv-tip: I have freaked out with csv in plain text!

By the way, I'm
using AT13, so I don't know if I need to apply a bugfix to this you say
or you refer to following versions.


On Wed, 17 Jul 2013 08:28:09
-0400, Jason Swails wrote:

> On Wed, Jul 17, 2013 at 5:44 AM, Fernando
Martín García wrote:
>> Dear Amber users, I'm trying to perform a
decomposition per-residue of my system (protein+DNA) using the following
input file: Input file for running PB and GB &general endframe=10,
verbose=1, / &gb igb=2, saltcon=0.100 / &decomp idecomp=1,
> Make sure you are printing at least one residue from
the receptor and one residue from the ligand. This should be fixed in
the next version, but may not be for yours. Also, make sure that you
apply all bug fixes (and I suggest using AmberTools 13), otherwise you
may get some ugly formatting in the output file. Note that for
AmberTools 12 and 13, the default output file is CSV-formatted for easy
viewing in a spreadsheet program (although setting csv_format=0 in the
&decomp section will fix this). HTH, Jason

 Fernando Martín
 Molecular Modeling Group - Lab 312.1 
 Molecular Biology
Center "Severo Ochoa" 
 C/ Nicolás Cabrera, 1. 
 UAM University.
Cantoblanco, 28049 Madrid. Spain. 
 TEL: (+34) 91-196-4662 FAX: (+34)
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Received on Wed Jul 17 2013 - 06:00:06 PDT
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