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[ccp4bb]: pi-cation interaction in Refmac
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Thank you all for the suggestions about my question (below) related to
pi-cation interactions in Refmac.
In summary I got two different suggestions:
1) To turn off van der waals interactions for the nitrogen atom
of the ligand.
In PROTIN this can be done using the keyword VDWRADII
2) fix distances for all pi-cation interactions.
In PROTIN this can be done using the keyword SPECIAL.
Cristy
> Dear CCP4bb members
>
> I am refining a protein-ligand complex where the main
> interactions
> between those are hydrophobic and a cation-pi interaction between a
> nitrogen and a Phe ring.
>
> I used MAKEDICT to create a dictionary for my ligand, but
> because of
> the cation-pi interaction, REFMAC pushes protein and ligand apart.
>
> Is there any way to turn off the energy terms only for my
> ligand or it would be better to add the cation-pi interaction into the
> dictionary, if so, how do I do that?
>
> Thanks all
>
>
> Cristy
>
>
> *******************************
> Maria Cristina Nonato, PhD
> Chemistry and Chemical Biology
> Cornell University
> mcn22@cornell.edu
> phone:+1.607.255.6145
> *******************************
>