Structure minimization
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
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
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@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.h...
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
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@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
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@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@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.h...
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
Right, it is just standard minimization as described here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html> "It is intended for cleaning up small molecule structures and improving localized interactions within larger systems. It may not be able to resolve large-scale distortions or widespread structural problems. By definition, energy-minimization simply moves the system toward a local minimimum without crossing energy barriers, and does not search for the global minimum." On Jan 15, 2013, at 9:31 AM, Bobo Dang wrote:
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 Jan 15, 2013, at 8:20 AM, Bobo Dang wrote:
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?
There are other issues with your structure that you included in your bug report (and I will be getting back to you on those) but one thing I can say immediately and that is of general relevance is that if you modify a standard residue then you have to change the residue name. Chimera assigns atom types and charges to standard residues (i.e. a residue with a standard name) by using a template -- and such atom types and charges will not be correct if the residue has been modified. Furthermore, the underlying MMTK minimization code also uses templates for standard residues and expects all the normal atoms and bonds to exist. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
participants (3)
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Bobo Dang -
Elaine Meng -
Eric Pettersen