[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


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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

Mengbin Chen
Department of Chemistry
University of Pennsylvania
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20130613/c3693901/attachment.htm>

More information about the phenixbb mailing list