On Thu, Oct 20, 2022, Huang ZiJian via AMBER wrote:
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 600 -2.5309E+07 2.6984E+10 6.8559E+12 OD1 1353
>
> BOND = 8585.4915 ANGLE = 1006.2007 DIHED = 3823.9176
> VDWAALS = 12025.1277 EEL = -184709.9835 HBOND = 0.0000
> 1-4 VDW = 1146.7754 1-4 EEL = ************* RESTRAINT = 0.0000
>It seems that the corresponding aspartate residue and water molecule
>which are connected to the same magnesium ion cause structure
>distortion. Although I delete related bonds in the LEaP modeling, treating
>the bonds in a nonbonded way as suggested in the tutorial, it doesn't work
>well.
Can you clarify things here? What exactly did you do to "delete related
bonds in the LEaP modeling"?
Second, if you treat things as non-bonded (which would be the "normal"
procedure) what symptoms do you see that makes you think "it doesn't work
well"?
...thx...dac
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Received on Thu Oct 20 2022 - 09:00:02 PDT
