I am trying to create a protonated cytidine residue in Amber. I have
been able to calculate charges for the individual atoms. When I enter
the atom types and charges and then try to check it I get an error
"cannot find angle parameter: CM - CA - NA" and "cannot find angle
parameter: N* - CM - HA". This would represent the C5 - C4 - N3 and N1
- C6 - H6 atoms, respectively. I think that I might have chosen the
wrong atom types. I used the following atom types for the base:
N1 - N*; C2 -C; N3 - NA; C4 - CA; N4 - N2; C5 - CM; C6 - CM; H3 - H;
H41 - H; H42 - H; H5 - HA; H6 - HA
My first question is have I used the wrong atom types? My second
question is can I enter the angle parameter or create a new atom type?
or does someone have a library for a protonated cytidine?
Thanks,
Peter
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Received on Wed Aug 10 2005 - 16:53:00 PDT
