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:ytu@mix.wvu.edu] Sent: 16 November 2004 07:08 To: modeller_usage@salilab.org 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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