Hello, I used :/!isHet for the "spec" option for "minimize" and I'm still getting "Unable to find GAFF type for #0:155.A@FE " for 101M. I thought this would skip the heme, but I guess not. How can I avoid this error? Thanks again! Alex On Tue, Jul 14, 2009 at 5:07 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Alex, If by standard you mean non-HETATM, then you could use Chimera command

select ~ :/isHet

or for protein and nucleic acid molecules only,

select protein | nucleic acid

If you mean "residues that are in the amber parm file and thus don't require running antechamber" I don't know of a command-line specifier for exactly that, although the above may work in many cases. However, if you use minimize with the nogui option, it can handle those nonstandard residues without raising a dialog, as described in the "minimize" page: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html>

For your hydrogen question, if you mean you want to allow only hydrogens to move, yes, that general approach will work. Be aware that the command you showed, however, selects only atoms named H, which for proteins are just the amide hydrogens. If you want to select all atoms of element H, it would be

select H

or if you want to select only polar (thus possibly H-bonding) hydrogen atoms, it would be

select @/idatmType=H

(type HC is hydrogens bonded to C, type H is all the other hydrogens) Atom type descriptions: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html>

I don't know what is going on with the missing object error. Certainly it does not occur every time DockPrep deletes atoms, and it probably depends on something specific in the structure you are working with.

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

On Jul 13, 2009, at 5:29 PM, Alex Gawronski wrote:

Hello,

...

Is there a way to select only standard residues with the "select" command?

I was also wondering if this would work to minimize only H bonds: runCommand('select @H') runCommand('minimize freeze unselected nogui true')

If not, how can it be done? When I try the inverse (selecting everything before Hs are added), I get "ValueError: underlying C++ Atom object is missing", which I assume occurs because atoms are removed by Dock Prep.

Thanks in advance!

Alex Gawronski Carleton University _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev