[AMBER] MCPB

From: Jinqiang <hjq2012.hotmail.com>
Date: Thu, 11 Jul 2013 11:54:06 -0400

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 Thu Jul 11 2013 - 09:00:05 PDT
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