AMBER Archive (2009)

Subject: Re: [AMBER] bond length energy

From: Mark Williamson (mjw_at_sdsc.edu)
Date: Wed Jun 17 2009 - 12:29:09 CDT

Thomas Lake wrote:
> Hi,
>
> Is there a function for calculating the bond length energy between a
> pair of atoms in a molecule? In my case I want to calculate the bond
> length energy of a disulfide (S-S) bond, as a function of time. I can
> calculate the bond distance using ptraj.
>
> Thanks
>
> Thomas Lake
> Imperial College London
>

Hi Thomas,

If you want to know the energy contribution from *only* the two body
bonding term, and know the length of this bond as a function of time and
its parameters, then you have all you need to calculate its potential
energy:

amber11/dat/leap/parm$ grep -e ^"S -S" parm99.dat
S -S 166.0 2.038 JCC,7,(1986),230; CYX (SCHERAGA)

$ cat /tmp/distance_output_from_ptraj.dat
2.2
2.1
2.3
2.4
etc....

$ awk < /tmp/distance_output_from_ptraj.dat '{print 166.0*($1-2.038)**2 }'
4.3565
0.638104
11.3949
21.7533
etc...

regards,

Mark

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