Minimizing the structure in Chimera
Dear Mr. or Mrs. I am trying to minimize a structure of mutated coEnzyme B but the program gives me this error
Dear Mr. or Mrs. I am trying to minimize a structure of mutated coEnzyme B but the program gives me this error Element Ni (atom #0:700.A@NI) is not currently supported [no GAFF type] Best regards, Elias Veijola
Dear Elias Veijola, Sorry, there are only parameters for a certain set of elements.
From the Minimize Structure manual page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html>
"Monatomic ions are assigned user-specified net charges and Amber VDW parameters. The following ions are handled: Li+, Na+, K+, Rb+, Cs+, F–, Cl–, Br–, I–, Mg2+, Ca2+, Zn2+. In addition, Fe ion nonbonded parameters are taken from the heme residue in the Amber parameter database. See Limitations for how to add types.” It is very difficult to try to add parameters yourself, but you take a look at the Limitations section if you want: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#limitations> If you are not trying to be highly precise or the Ni ion is not near the parts of interest, you could consider text-editing your input file to change it to a different metal (one in the list above) or even delete it entirely. Best regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 31, 2018, at 2:16 AM, Veijola Elias <elias.veijola@aalto.fi> wrote: Dear Mr. or Mrs. I am trying to minimize a structure of mutated coEnzyme B but the program gives me this error Element Ni (atom #0:700.A@NI) is not currently supported [no GAFF type] Best regards, Elias Veijola
Dear Elaine, Thank you for the respond. Yes I tried to overcome the problem with your suggestions but it didn't work. However I just deleted the whole metal ion complex and that solved the problem. Atleast it can be used as an visual suggestion for my future project. Best regards, Elias Veijola ________________________________ Lähettäjä: Elaine Meng <meng@cgl.ucsf.edu> Lähetetty: 31. tammikuuta 2018 18:21:00 Vastaanottaja: Veijola Elias Kopio: chimera-users@cgl.ucsf.edu Aihe: Re: [Chimera-users] VL: Minimizing the structure in Chimera Dear Elias Veijola, Sorry, there are only parameters for a certain set of elements.
From the Minimize Structure manual page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html>
"Monatomic ions are assigned user-specified net charges and Amber VDW parameters. The following ions are handled: Li+, Na+, K+, Rb+, Cs+, F–, Cl–, Br–, I–, Mg2+, Ca2+, Zn2+. In addition, Fe ion nonbonded parameters are taken from the heme residue in the Amber parameter database. See Limitations for how to add types.” It is very difficult to try to add parameters yourself, but you take a look at the Limitations section if you want: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#limitations> If you are not trying to be highly precise or the Ni ion is not near the parts of interest, you could consider text-editing your input file to change it to a different metal (one in the list above) or even delete it entirely. Best regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 31, 2018, at 2:16 AM, Veijola Elias <elias.veijola@aalto.fi> wrote: Dear Mr. or Mrs. I am trying to minimize a structure of mutated coEnzyme B but the program gives me this error Element Ni (atom #0:700.A@NI) is not currently supported [no GAFF type] Best regards, Elias Veijola
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Veijola Elias