ADL: Parameters for phosphorus atoms?

Ruth Huey rhuey at
Thu Feb 10 11:48:02 PST 2005

SRMD, Col - Platt, Steven wrote:

>Dear List,
>I'm reading in a protein/DNA complex (MOL" format) as a static
>macromolecule, with the aim of creating a grid, etc... but ADT comes up with
>the error 
>"macromolecule has an unusual atom type: P
>Do you want to add this type which means changing 
>P to M and defining new energy parameters?"
>This brings up 2 questions...
>1)       I thought AutoDock recognised P (phosphorus) as a legitimate atom
>type. Is this not the case?
Hi Steve,
In the macromolecule pdbqs file, the P atoms must be renamed using one 
of the 2 'wildcards' recognized by AutoDock...
The problem is that AutoDock3 allows the macromolecule to have atom 
types CNOSHXM <and that's all!>... so if your macromolecule has other 
atomtypes, for instance P,
    (1) you must write a pdbqs file where the P is renamed... for 
instance if it was P17, it would be renamed M17
    (2) you must write a gpf file which has the correct corresponding 
values for "M"....for instance, in the section defining the energy 
parameters for the carbon map:

map                       # atom-specific affinity map
nbp_r_eps  4.00 0.0222750 12  6   # C-C lj
nbp_r_eps  3.75 0.0230026 12  6   # C-N lj
nbp_r_eps  3.60 0.0257202 12  6   # C-O lj
nbp_r_eps  4.00 0.0257202 12  6   # C-S lj
nbp_r_eps  3.00 0.0081378 12  6   # C-H lj
nbp_r_eps  3.00 0.0081378 12  6   # C-H lj
nbp_r_eps  4.10 0.0257202 12  6   # C-M lj

ADT can write the appropriate pdbqs file [it is always worth while 
checking for the name substitution!].
For it to write the appropriate gpf file, you must supply the Rii and 
epsii values for the wildcard type you are defining [by typing the 
values into the widget which asks you if you want to define a new type.....]

>2)       What are correct parameters (Rij & epsij) for Phosphorus?
>ml>  suggests that "a very rough approximation for phosphorus parameters is
>to borrow those of carbon"... where would a novice like myself find this
If you look in the "" file in the AutoDockTools 
directory, you will find these values:
             Rij("P" "P")  = 4.20
             epsij("P" "P") = 0.2000 * FE_vdW_coeff  where 
<it's defined at the top of that file>
      or  epsij("P" "P") = 0.0297

<fyi: Rij("P" "C") = (Rij("P" "P") + Rij("C" "C"))/2  which is the 
arithmetic mean
        epsij("P""C") = sqrt(epsij("P" "P") *epsij("C" "C")) which is 
the geometric mean...>


>Many thanks
>Steve Platt
>Bioinformatics Support Co-ordinator
>Genomics, Proteomics & Bioinformatics Unit
>HPA Colindale
>61 Colindale Avenue
>NW9 5HT
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