[Chimera-users] Structure minimization

[Bobo Dang]

Got it, I  submitted a bug report with the pdb file I am working on.

One more thing, the minimize function in Chimera is just to give a
minimized structure in the local environment, it does not cross the energy
barrier to give the structure which has the minimum energy of the system,
is that right?

thank you

bobo

On Tue, Jan 15, 2013 at 10:44 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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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