AMBER Archive (2009)

Subject: Re: [AMBER] creating bond

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Jun 03 2009 - 13:32:57 CDT

On Wed, Jun 03, 2009, Jorgen Simonsen wrote:
>
> I have a problem that I would like to create bonds between an ion and
> different residue in a protein simulation. I have create lib-files and for
> my methionine I have included the Cu-ion but I have a cys residue as well
> that I would like create a bond between the Cu-ion and the sulfur but it
> seems that it doesn't recognize the bond.
>
> In the lib file my copper is included in the MEM residue like this
>
> "CU" "CU" 0 1 131075 18 29 0.289000
>
> and for the sulfur in my Cys it looks like this
>
> "SG" "SJ" 0 1 131072 8 16 -0.28400
>
> I then create a frcmod file with bond parameters etc like this for the
> copper interaction
> ## Modification
> MASS
> SJ 32.06
> CU 65.36
>
> BOND
> SJ-CU 5010.62 1.18
> CU-SJ 5010.62 1.18
> CT-SJ 203.0 2.21
>
> it can recognize the CT-SJ bond from this file if I increase the force
> constant to 2500 but it cannot recognize the SJ-CU - Any help or hinits
> appreciated thanks in advance

I'm not sure what "it" is (first word in the sentence above). The presence or
absence of a bond has nothing to do with its force constant (and the above
values are way to large.) To create bonds that are not in the library (such
as bonds between residues) you need to use the "bond" command in LEaP.

...dac

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