[Chimera-users] read dcd from openMM simulations

Eric Pettersen pett at cgl.ucsf.edu
Tue Nov 22 13:14:40 PST 2016

Hi Michał,
	You can write a prmtop for any open structure in Chimera using the Write Prmtop tool (in the Amber category).  Now, that tool is designed to work with normal organic molecules, whereas your “molecule” is a linear chain of 10 boron atoms, so you are going to have to set partial charges and GAFF atom types “by hand” before running Write Prmtop instead of letting Chimera try to figure them out (which ultimately won’t work).  So, you need to execute these two commands before running the tool

	setattr a charge 0
	setattr a gaffType c3

Then you can run the tool.  You’ll get a dialog complaining about incompatibilities with the force field.  Just ignore it (i.e. click “Continue Anyway” on the dialog).  Then you will be able to write a prmtop that you can use with your DCD file.


	Eric Pettersen
	UCSF Computer Graphics Lab

P.S.  If your didn’t mean for the boron atoms to form a chain, you should use HETATM instead of ATOM records in your PDB file.

> On Nov 22, 2016, at 7:31 AM, Michał Kadlof <m.kadlof at cent.uw.edu.pl> wrote:
> Is there any way to read dcd trajectory from openMM simulation?
> Example in attachment.
> OpenMM does not produce psf or prmtop files :(
> --
> pozdrawiam serdecznie
> Michał Kadlof <m.kadlof at cent.uw.edu.pl <mailto:m.kadlof at cent.uw.edu.pl>>
> <micro-poli.pdb><output.dcd>_______________________________________________
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