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 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@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@cent.uw.edu.pl <mailto:m.kadlof@cent.uw.edu.pl>> <micro-poli.pdb><output.dcd>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users