AMBER Archive (2008)

Subject: Re: AMBER: converting from CNS file format

From: Sally Pias (sallypias_at_gmail.com)
Date: Fri Apr 11 2008 - 00:04:55 CDT

For the record, I was able to find a database called the BioMagResBank
(BMRB), where NMR data from Protein Data Bank records have been parsed
and archived in a uniform format. These data can be "converted" and
downloaded from the BMRB in various file formats, including DIANA
format. The URL for the database is http://www.bmrb.wisc.edu/ , and
one should select the "Restraints" menu option to obtain parsed and
reformatted restraints using a given PDB identifier. The current
location of the restraints database is
http://tang.bmrb.wisc.edu:8080/WebModule/MRGridServlet . I hope this
is of help to others.

Sally Pias

On Tue, Apr 8, 2008 at 11:32 PM, Sally Pias <sallypias_at_gmail.com> wrote:
> 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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