RE: [modeller_usage] wrong topology for the ligand?

["Higueruelo Alicia (CAM)" <>]

Hi Youbin,

In my experience,(please someone correct me if I'm wrong) the ligands in
modeller don't look great, my guess is that CHARMm deals really well with
aminoacids but struggle a bit with non-aminoacid atom types. (or a least the
version I'm using).

But they look reasonable. If the ligand look really really weird. try to
compare the "PDB atom names" in your template ( the pdb file you are using
to built your model) and the "PDB atom names" in your top_heavy.lib. Hope
the following lines are a good example.

in top_heav.lib in RESI LIG  "ATOM O1 OE -0.10000"
in template.pdb  "ATOM 4000  O1   LIG D 500  30.722 47.505 16.832"

To have the same connection and geometry in the model-ligand than in the
ligand-template, these PDB names should be the same "O1", I think this is
what is telling Modeller where to put the atom (assigning the xyz coords
from atom called O1 from the LIG in the PDB), and "OE" is the CHARMm atom
type to use the potentials .

In my output files, my model does not have connection data in the pdb,
therefore the way you see you models depends which software you are using to
visualize your pdb, again, lots of them can not guess that a phenyl ring
(not in a aminoacid) has alternate double bounds or aromatic bonds, and
display them in funny ways. There are spl macros in sybyl for example, which
will fix some of these problems, based on the geometry of the ligands. but
I'm not aware of a 3D viewer which display chemically correctly all ligands
in pdb format. 

Hope this is useful,

any comments on that more than welcome,

cheers,

alicia


-----Original Message-----
From: Youbin Tu [">mailto:]
Sent: 16 November 2004 07:08
To: 
Subject: [modeller_usage] wrong topology for the ligand? 


Hi all:

     I am using MODELLER7V7 to build a ligand-enzyme complex, I created 
the ligand and modified the library files. Everything worked well 
except the ligand in the final result seems too weird, for example the 
benzene is not planar and there are many bonds between 2 atoms which 
should only have one bond theoritically. 
     I thought maybe it is my problem when building the ligand. But 
when I tried to use GDP which  already existed in the library file. The 
final 
results still have the same problem. 
     Anyone knows how to deal with this kind of problem? Does it mean 
that we have to modify the par.lib or make restraints for bonds of the 
ligands? If so, can you tell me how to do that,any softwares are 
available for that purpose? 
      Your reply is highly appreciated. 

                                                                   
youbin

                                                              



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