AMBER Archive (2009)

Subject: [AMBER] makeDIST_RST: no map function for ambiguous restraint

From: Peter Varnai (p.varnai_at_sussex.ac.uk)
Date: Sun May 17 2009 - 13:41:24 CDT

Hello,

I use makeDIST_RST to create normal and ambiguous restraints. Since no
standard map file is provided for sugars, I created one that maps all
atoms of the residues in a molecule and then I added at the end if
this file some ambiguous definitions of this form:

RESIDUE VLB
MAPPING C1 = C1
MAPPING H1 = H1
MAPPING O5 = O5
MAPPING C5 = C5
MAPPING H5 = H5
MAPPING C6 = C6
MAPPING O6 = O6
MAPPING H61 = H61
MAPPING H62 = H62
MAPPING C4 = C4
MAPPING H4 = H4
[...]
MAPPING H2O = H2O
MAPPING O3 = O3
#
AMBIG l5 = H4 8 H2 11 H2 17

I use the 8-column format for the input file:
# normal
20 3LB H1 5 VLB H1 1.8 6.0 #4.04-6.83
# ambiguous
5 VLB H1 0 AMB l5 1.8 6.0

The following command gives error message:
makeDIST_RST -pdb prep.pdb -ual noe.prep -map sugar.map -rst out.noe
# makeDIST_RST
Currently configured for up to 5000 atoms
Using MAP file sugar.map
read_maplib:3LB l5 to (H4 8); (H2 11); (H2 17);
ERROR no map function for l5 AMB :data= 5 VLB H1 0 AMB l5 1.8 6.0

I obtain out.noe that has all normal restraints but not the ambiguous
one. I checked in each case that the atom names exist in the given
residue number and it has entry in the map file; eg, residue 8 is VLB
that has atom named H4 which has a MAPPING line.

Is this the correct way of producing ambiguous restraints? I can
provide the necessary files if needed.

A further question how to deal with a given cross-peak that was
assigned to three atom-pairs A-X or B-Y or C-Z. The AMBIG definition
requires to create two groups A,B,C and X,Y,Z but that would allow for
all possible distances to contribute to the ambiguous restraint not
only the three above.

Thanks very much.

Peter

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber