[buster-discuss] Question about ligands

[Miguel Ortiz Lombardia]

Hi,

I have a question about the proper treatment of ligands that have  
already a dictionary in the TNT library. In my case it's a sulfate  
(SO4) residue. If I do nothing, gelly complains. I quote from the log  
file:

> Have matched 14 residue-type records and will use 18 ccp4 energy  
> atomtypes
> Have no dictionary entry giving ccp4 atom types for residue types: SO4
> 	will use default ccp4 atom types CUNK NUNK OUNK PUNK SUNK ....  
> where possible.
> All atoms matched for ccp4 atom type - so ideal contact will be used  
> for all contacts (rather than TNT short).
This is somehow confusing, since the SO4 residue seems to be found in:

$BDG_HOME/tnt/data/ccp4/SO4.dic
$BDG_HOME/tnt/data/msd/SO4.dic

and also,

$BDG_HOME/tnt/data/assume.dat

includes this line:

ASSUME  RESIDUE_TYPE  SO4  WHEN_CONTAINS  S O1 O2 O3 O4

These are the atom names in my pdb file.
Indeed, if I copy the dictionary from:

$BDG_HOME/tnt/data/ccp4/SO4.dic

to a file that I give to refine with the -Gelly option, I get an error  
message:

>  Check for duplicate bonds: DUPLICATES FOUND
>    Have duplicate bonds between atoms C|1:O1 (SO4) C|1:S (SO4):
>    ideal distance=   1.465 sigma=   0.041
>    ideal distance=   1.460 sigma=   0.020
>    Have duplicate bonds between atoms C|1:O2 (SO4) C|1:S (SO4):
>    ideal distance=   1.465 sigma=   0.041
>    ideal distance=   1.460 sigma=   0.020
>    Have duplicate bonds between atoms C|1:O3 (SO4) C|1:S (SO4):
>    ideal distance=   1.465 sigma=   0.041
>    ideal distance=   1.460 sigma=   0.020
>    Have duplicate bonds between atoms C|1:O4 (SO4) C|1:S (SO4):
>    ideal distance=   1.465 sigma=   0.041
>    ideal distance=   1.460 sigma=   0.020
>
> WARNING potential angle C|1:O1(SO4)=C|1:S(SO4)=C|1:O2(SO4) has two  
> or more angle restraints defined, numb=    2
> WARNING potential angle C|1:O1(SO4)=C|1:S(SO4)=C|1:O3(SO4) has two  
> or more angle restraints defined, numb=    2
> WARNING potential angle C|1:O1(SO4)=C|1:S(SO4)=C|1:O4(SO4) has two  
> or more angle restraints defined, numb=    2
> WARNING potential angle C|1:O2(SO4)=C|1:S(SO4)=C|1:O3(SO4) has two  
> or more angle restraints defined, numb=    2
> WARNING potential angle C|1:O2(SO4)=C|1:S(SO4)=C|1:O4(SO4) has two  
> or more angle restraints defined, numb=    2
> WARNING potential angle C|1:O3(SO4)=C|1:S(SO4)=C|1:O4(SO4) has two  
> or more angle restraints defined, numb=    2
>    There are not any bad contacts where Delta/sigma is greater  
> than     6.5
>    Worst contact dist=   2.507 std=   3.400 sigma=   0.200 abs(Delta/ 
> sigma)=    4.465 ats A|7:O (ARG) A|11:SG.B (CYS)
>    It is likely that the geometry libraries, sequence info and links  
> match the input molecule
>  GEOMETRY CHECK OVERALL:  PASS
>
>   Have -type card that specifies calculation type 'screen'
>
>  -screen_sigma option: will do screen, outputting deviations up to  
> delta/sigma cutoff   5.000
>  -screen option: max number of reports in screen output set to     720
>  Writing restraints screen output to file: 6c/01-BUSTER/Cycle-1/ 
> gelly_screen.lis
>       (filename specified by -screen_file)
>  s/r gelly normal termination
>



I dag this out and found that indeed the dictionary coming from the  
ccp4 directory in tnt and the definitions found in:

$BDG_HOME/tnt/data/othergeo.dat

are actually different. But beyond that there are three puzzling  
issues here:

1. The fact that the restraints are doubled seems to imply that SO4  
was actually recognized and assigned the appropriate atom types (and  
not SUNK, OUNK) in spite of the original message from gelly.

2. Why libraries with different values are present in BUSTER-TNT?

3. In the last listing, you can see "GEOMETRY CHECK OVERALL:  PASS".  
However, the program stops...

I would appreciate if you can clarify a bit on these and also tell me  
which is the proper way of refining in the presence of these type of  
ligand.

Thanks a lot!
Best regards,



-- Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombardia at afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2





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