[Chimera-users] Structure minimization

[Bobo Dang]

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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