[Chimera-users] Structure minimization

Elaine Meng meng at cgl.ucsf.edu
Tue Jan 15 08:44:01 PST 2013


Hi Bobo,
Instead of sending email here, we recommend reporting problems by using "Help... Report a Bug" in the Chimera menu and attaching the data (PDB or Chimera session file) needed to reproduce the problem.  Also include a full description of steps needed to reproduce the problem, and your email address if you wish a response.   Problems like these are not possible to understand without the specific data.

In this case, the messages show it is running semi-empirical charge calculation using the Antechamber package (which is included with Chimera).  I don't see anything about a failure.  Maybe it is just taking a long time.  Or if it fails, it may be that this method (choice AM1-BCC in the add charge dialog) cannot handle your specific nonstandard residue.  You might try choosing the other charge calculation option, Gasteiger (generally faster and more approximate), which may allow you to proceed.

Best,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 15, 2013, at 8:20 AM, Bobo Dang wrote:

> Dear Elaine,
> 
> I was trying to use Chimera to minimize a structure I modified and I got the following result. It seems that Chimera was not able to assign the charge to the modified Phe residue (I added one sulfur atom at the beta position of this Phe reidue), do you know how I can fix it?
> 
> 
> (UNK+PHE) Running: /Applications/Chimera.app/Contents/Resources/bin/amber11/bin/sqm -O -i sqm.in -o sqm.out
> 
> (UNK+PHE) Error: cannot run "/Applications/Chimera.app/Contents/Resources/bin/amber11/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
> 
> (UNK+PHE) Running: /Applications/Chimera.app/Contents/Resources/bin/amber11/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
> 
> (UNK+PHE) 
> 
> (UNK+PHE) Running: /Applications/Chimera.app/Contents/Resources/bin/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
> 
> 
> Thanks
> 
> bobo
> 
> On Mon, Jan 14, 2013 at 11:52 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Bobo,
> As far as I know, yes.  Just try.  8-)
> 
> Nonstandard residues will be parametrized automatically as described here:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#parameters>
> 
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Jan 14, 2013, at 9:46 AM, Bobo Dang wrote:
> 
> > Hey All,
> > I am trying to use Chimera to minimize a small protein with a special structure, the model has nonstandard amino acid,
> > Also the N-terminal is connected to cyclized to one Asp side chain, is it possible to minimize this modified structure by
> > Chimera?
> > Thanks
> > bobo




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