[phenixbb] elbow

Mengbin Chen mengbinc at sas.upenn.edu
Thu Jun 13 12:50:58 PDT 2013


Hi Nat,

So I added SMILES in Chemical string, but the conformation came out to be
different than the input pdb file, even "none" was chosen for geometry
optimization.

Mengbin


On Thu, Jun 13, 2013 at 3:20 PM, Nathaniel Echols <nechols at lbl.gov> wrote:

> On Thu, Jun 13, 2013 at 11:53 AM, Mengbin Chen <mengbinc at sas.upenn.edu>wrote:
>
>> I tried the command line in Terminal, but Elbow still regularized the
>> conformation and bonds of the ligand and the result turned out to be the
>> same with that I ran thorough GUI. The thing is that the input pdb file has
>> a conformation the ligand should adopt so that I do not really want energy
>> minimization or geometry optimization to be done on it. Although I set
>> "none" for "geometry optimization" in GUI, it unfortunately changed the
>> ligand conformation.
>>
>
> This has nothing to do with use of the GUI versus command line - the
> problem is that using a PDB file as the only source of chemical information
> is unlikely to work, especially if no hydrogens are present.  At the very
> least you need explicit hydrogens, and ideally you need an input file that
> actually defines the topology, like SMILES or MOL2 or CIF.  If it's a
> ligand that is already in the PDB you can just give it the three-letter
> code and it will extract this information automatically from the database
> included with Phenix.
>
> I guess I need to add a warning to the GUI if users try to use a PDB file
> alone, because this problem comes up again and again.
>
> -Nat
>
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>


-- 
Mengbin Chen
Department of Chemistry
University of Pennsylvania
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