AMBER Archive (2008)

Subject: AMBER: converting from CNS file format

From: Sally Pias (sallypias_at_gmail.com)
Date: Wed Apr 09 2008 - 00:32:11 CDT

Hello, everyone.

I have a set of NMR distance restraints that were generated using CNS.
 The set contains a large number of peak "ambiguities" arising from a
lack of stereospecific assignments. Converting the CNS notation for
ambiguities to Amber notation (similar to the file format used by
DIANA and DISGEO) is a daunting task to do by hand, and I was
wondering if anyone knows of an existing a program to accomplish this
conversion.

(CNS uses a hashmark notation to indicate ambiguities. For example,
HB# means "either HB1 or HB2." In Amber notation, I believe this
ambiguity would be indicated using the following lines in the MAP
file:

AMBIG HB#:A = HB1 RES1 HB2 RES1 HB3 RES1
AMBIG HB#:xA = HB2 RES1 HB3 RES1

The first line would be used for any ALA residue with the HB#
ambiguity, while the second line would be used for non-alanine
residues.
To generate the MAP file lines for every ambiguity would require
coordinating the CNS ambiguities for each residue type with the
residue topology used in the Amber force field. There are about 5
different kinds of ambiguities per residue type -- not an impossible
task to do by hand, but certainly time-consuming.)

I have already converted everything except the ambiguities in the NOE
list to the "8 column distance bound" file format used by Amber. The
following are a few lines from my current NOE list, showing the NOE
distance constraints for two residues. You will notice that there are
a lot of ambiguities per residue:

17 GLN HE21 17 GLN HB# 3.8 6.3
17 GLN HG# 17 GLN HE21 1.3 3.8
17 GLN HG# 17 GLN HE22 2.8 5.3
17 GLN HG# 17 GLN H 1.3 3.8
17 GLN HB# 17 GLN H 2.3 4.8
17 GLN HA 17 GLN H 2.3 3.8
17 GLN H 17 GLN HE21 1.8 3.3
17 GLN H 18 LEU HA 2.3 5.3
17 GLN H 18 LEU HB# 2.3 6.3
17 GLN HE22 18 LEU HB# 1.8 6.8
17 GLN H 18 LEU H 0.8 3.8
17 GLN HG# 18 LEU H 2.3 6.3
17 GLN HB# 18 LEU H 2.3 6.3
17 GLN HA 18 LEU H 0.8 3.8
17 GLN HE22 18 LEU H 2.3 5.3
17 GLN HE21 18 LEU H 1.8 4.8
17 GLN HE21 17 GLN HG# 1.8 3.8
17 GLN HE22 17 GLN HG# 1.8 5.3
17 GLN HA 17 GLN HB# 1.8 4.3
17 GLN HG# 17 GLN HB# 1.8 5.3
17 GLN HB# 18 LEU H 1.8 6.3
18 LEU HD2# 18 LEU H 1.8 5.1
18 LEU HD1# 18 LEU H 1.8 6.1
18 LEU HB# 18 LEU H 1.8 4.3
18 LEU HB# 18 LEU H 1.8 4.3
18 LEU HA 18 LEU H 1.8 3.8
18 LEU H 19 TRP H 1.8 5.3
18 LEU HA 19 TRP H 1.8 3.3
18 LEU HD# 19 TRP H 1.8 8.2
18 LEU HD# 20 PHE HB# 1.8 7.7

Any help with this problem would be appreciated.

Best,
Sally Pias
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