[Chimera-users] Preparation of the protein-ligand system for the amber simulation

Eric Pettersen pett at cgl.ucsf.edu
Wed Apr 30 11:54:40 PDT 2014

Hi James,
	It depends a little on what "system preparations" means to you, but if you mean "clean up for MD/docking" by eliminating alt locs, adding missing side chains, assigning charges, etc. then yes you can.  The following two-line script will take the currently open model and run a "zero step" minimization on it (thereby only preparing it for minimization) and then write out a mol2 file named "prepped.mol2: in your home directory:

minimize nsteps 0 cgsteps 0
write format mol2 0 ~/prepped.mol2

You may want to look at the documentation for the 'minimize' and 'write' commands to see if there are any other options you'd also want to use.
	If the above lines were in a file named "prep.cmd" the you could prepare 3FX2 with:

chimera --nogui pdb:3fx2 prep.cmd

	Obviously you must want to do this on a lot of files, so you should look at the page in the programmer's guide that discusses looping through data files and performing commands such as the above on them:

Very Basic Chimera Programming Primer

I think it's pretty clear how you would adapt the example given in the primer to use the commands you need.  If you need further help though just ask.
	If your original question means something else though, like writing out a prmtop file, that's possible but quite a bit more complicated -- so I'm not going to go into that here unless you say something. :-)


                        Eric Pettersen
                        UCSF Computer Graphics Lab

On Apr 30, 2014, at 3:21 AM, James Starlight <jmsstarlight at gmail.com> wrote:

> Hi Elaine,
> thanks for suggestions. Could you tell me if it's possible to use some scripts to make system preparations using amber parameters without Chimera's GUI?
> James
> 2014-04-30 1:43 GMT+04:00 Elaine Meng <meng at cgl.ucsf.edu>:
> Hi James,
> I believe not - one of the main limitations is that there is very little ability to use anything other than the parameters you get from the force field choices listed in the dialog for standard residues and the Antechamber process automatically used for nonstandard residues (i.e. small molecules).  You can only substitute in different partial charges for nonstandard residues, and even that is rather  labor-intensive:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#limitations>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#user-specified>
> 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 Apr 29, 2014, at 3:45 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> > Dear Chimera Users,
> > I wounder to know if it's possible to use combination of the amber ff with the cgenff for the both parametrization of the small ligands in complex with the proteins using amber tools built in Chimera's? Does it possible to use some scripts instead of GUI for such tasks ? I'll be thankfull for some tutorial or example
> > Thanks for help,
> > James
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