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Department of Chemistry and Chemical Biology |
Questions and problems?WaterIn 'amber41/dat/parm91.dat' there is no angle bending parameter defined for HW-HW-OW. Is it appropiate to take the missing values from 'parm94.dat':HW-HW-OW 0. 127.74 (found in crystallographic water with 3 bonds) Dave Case & Bill Ross: Yes...when you use "crystallographic" waters (entered as WAT in the link step) an angle is defined as above, which needs a parameter. (This angle is not generated when waters are generated by the BOX option of AMBER). Note that the force constant above is zero, so this angle is not "really" there (i.e. always has zero energy because of the HW-HW bond which, with the use of SHAKE on H, keeps water rigid) but is necessary in some applications to include it in the parm.dat file. I believe that its absence from parm91.dat was an oversight. Web Masters <webadmin@www.amber.ucsf.edu> Last modified: Tue Nov 15 18:50:23 1994 |
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