[modeller_usage] A followup question to Re: questions on loopmodel in the presence of a ligand

[Diane Lynch DLLYNCH <>]

Hi, 

I understood that modeler will assign the radii based on the element in the BLK residue (since there are no parameters or topology for it, e.g. question 1 below).

But I think I am misunderstanding how exactly modeler assigns radii for BLK residues, because
when i put the following in my python script.

m.write(file='outGRASP.pdb', model_format='GRASP')

the GRASP.pdb file output has the radii 1.70 for all the atoms in my BLK ligand,e.g. in the outGRASP.pdb for one of the ligand atoms:

HETATM 2643  C1  CP5 B 334      -6.583   0.667  16.488  1.70  0.000

e.g. it seems to be assigned the radii of an UNDF atom (not a C atom?)

For clarification, how does modeler assign radii (from the radii.lib file) for BLK residues? 

And maybe there are some comments on whether this makes much difference in any case?

Thanks in advance -
Diane

-----Modeller Caretaker "><> wrote: -----

To: Diane Lynch DLLYNCH "><>
From: Modeller Caretaker "><>
Date: 07/02/2010 06:29PM
cc: ">
Subject: Re: [modeller_usage] questions on loopmodel in the presence of a ligand

On 6/30/10 11:43 AM, Diane Lynch DLLYNCH wrote:
> We have been using the loop modeling functionality (loopmodel class of
> modeller, mostly 8v2 but recently upgraded to 9v8) to add loops onto our
> receptor.
...
> The script is below and it runs sucessfully. From this i can generate
> loops that seem to recognize that the ligand is there

This is probably just luck - the loopmodel protocol does not consider
loop-ligand interactions (other than soft-sphere clashes - see below),
so the loop could certainly interact poorly with the ligand (e.g. it
won't preserve protein-ligand covalent bonds or other strongly
directional interactions). You could avoid this by overriding the
special_restraints() method to add whatever loop-ligand restraints you
think are appropriate.

> 1)How (using default settings, for example in the script below) does
> modeler decide what van der waal radii to assign the atoms in the ligand?

BLK ligands have no topology and no parameters, so Modeller has to guess
based on the name of each atom - for example it will guess that an atom
labeled 'C1' is a carbon and use the carbon radius defined in
modlib/radii.lib.

> I read about the loops and electrostatics/H's in
> http://salilab.org/archives/modeller_usage/2005/msg00244.html  which is
> pretty old, so I am not 100% certain things have not changed

That information is still accurate for the loopmodel protocol.

> 2)Given that the loop modeling routine uses a statistical potential, and
> is not necessarily parameterized to work well with
> electrostatics, does it assign default charges to the ligand?

No - Modeller does not use any kind of electrostatic potential, so even
if it did assign charges they wouldn't be used anyway.

> 3)Given that the loop modeling routine is not parameterized for H's. Is
> it better to remove the H atoms from the ligand as well?

I don't think it'll make a lot of difference in practice, since the soft
sphere radius of a hydrogen is pretty small, but you could certainly try
that.

     Ben Webb, Modeller Caretaker
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