Hi Jinqiang,
The force constants from the "sem" and "md" methods are known to be different, though without extensive investigation of the code I couldn't tell you why, mathematically, this is the case. Martin Peters, who originally wrote the MCPB code, could probably provide more information.
Practically, I've found that a combination of the two methods, in which the bond parameters come from the "md" file and angle parameters from the "sem" file, seems to work well. You're welcome to try various combinations and see how you get on.
Regards,
Ben
On 12/07/2013, at 3:54 AM, Jinqiang wrote:
> Hello all
>
>
>
> I am trying to follow the MCPB tutorial to do active site parameterization
> for 1AMP.
>
> Running genMetalFF.sh generated a few files including
> 1AMP_OH_sidechain_fc_md.bcl and 1AMP_OH_sidechain_fc_sem.bcl
>
> I am confused that '1AMP_OH_sidechain_fc_md.bcl' used Gaussian log file
> '1AMP_OH_sidechain_fc_md.log' as input to generate forcefield, while
> '1AMP_OH_sidechain_fc_sem.bcl' used Gaussian Formatted Checkpoint file
> '1AMP_OH_sidechain_opt_md.fchk' as input to generate forcefield.
>
> '1AMP_OH_sidechain_opt_md.fchk' was from Opt calculation while
> '1AMP_OH_sidechain_fc_md.log' was from Freq calcualtion. The frcmod files
> created by the two script have some inconsistency. More specifically, the
> force constants involving Zn are different. Please see attached.
>
>
>
> Could anyone explain this? Thanks very much in advance.
>
>
>
> Jinqiang Hou
>
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Received on Mon Jul 29 2013 - 02:00:03 PDT
