Following on new atom types (again)
Dear Chimera dev. Team, I'm trying to do the same as JD. The message that I receive is when I try to minimize is "Element Pt (atom #0.1.A@PT1) is not currently supported". As Mr Pettersen told me before, I defined the parameters of PT in heme-iron.frcmod file in ../bin/amber/dat/leap/parms and I also defined the "pt" atom in the MMTK Database. Then I added the charges without the covalent bond between the PT and its neighbours and finally I try to minimize with and without the bonds. Nothing happens. Probably I'm modifying the wrong files... Then, I have other question to you regarding the IDAM Type. When I minimize, the N3 atoms become N3+. How can I change it? Thank you so much for your time and your patience. -- Elisabeth Ortega Carrasco, Ph.D. Student Molecular Modelling of Transition Metal Systems Group Lab. C7/153, Chemistry Department Universitat Autonoma de Barcelona Tel.: +34935812857 email.: ortega.elisabeth@qf.uab.cat
Eric mentioned it, http://plato.cgl.ucsf.edu/pipermail/chimera-dev/2013/000948.html but to be more explicit, one way to change atom type is with the "setattr" command, for example: setattr a idatmType N3 sel (changes type for the currently selected atoms) Elaine On Mar 18, 2013, at 3:34 AM, Elisabeth Ortega wrote:
Dear Chimera dev. Team,
I'm trying to do the same as JD. The message that I receive is when I try to minimize is "Element Pt (atom #0.1.A@PT1) is not currently supported". As Mr Pettersen told me before, I defined the parameters of PT in heme-iron.frcmod file in ../bin/amber/dat/leap/parms and I also defined the "pt" atom in the MMTK Database. Then I added the charges without the covalent bond between the PT and its neighbours and finally I try to minimize with and without the bonds. Nothing happens. Probably I'm modifying the wrong files...
Then, I have other question to you regarding the IDAM Type. When I minimize, the N3 atoms become N3+. How can I change it?
Thank you so much for your time and your patience.
-- Elisabeth Ortega Carrasco, Ph.D. Student Molecular Modelling of Transition Metal Systems Group Lab. C7/153, Chemistry Department Universitat Autonoma de Barcelona
Tel.: +34935812857 email.: ortega.elisabeth@qf.uab.cat _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
On Mar 18, 2013, at 3:34 AM, Elisabeth Ortega wrote:
Dear Chimera dev. Team,
I'm trying to do the same as JD. The message that I receive is when I try to minimize is "Element Pt (atom #0.1.A@PT1) is not currently supported".
This means that the platinum atom does not have a "gaffType" attribute assigned. This attribute should have been assigned by AddCharge. If you are assigning the charges yourself, you need to assign some gaffType to the platinum (I guess I suggest: setattr a gaffType Pt Pt).
As Mr Pettersen told me before, I defined the parameters of PT in heme-iron.frcmod file in ../bin/amber/dat/leap/parms and I also defined the "pt" atom in the MMTK Database. Then I added the charges without the covalent bond between the PT and its neighbours and finally I try to minimize with and without the bonds. Nothing happens.
What does "nothing happens mean exactly? Does no minimization occur? Does a minimization occur but no atoms move? --Eric
Probably I'm modifying the wrong files...
Then, I have other question to you regarding the IDAM Type. When I minimize, the N3 atoms become N3+. How can I change it?
Thank you so much for your time and your patience.
-- Elisabeth Ortega Carrasco, Ph.D. Student Molecular Modelling of Transition Metal Systems Group Lab. C7/153, Chemistry Department Universitat Autonoma de Barcelona
Tel.: +34935812857 email.: ortega.elisabeth@qf.uab.cat _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
participants (3)
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Elaine Meng -
Elisabeth Ortega -
Eric Pettersen