Hello all,
I am interested in partial charge derivation of a polymer. I am using R.E.D III for this. I have a few questions regarding the set up:
1) I decided to derive the partial charge of one monomer and use those charges for each constituent monomer in the polymer. I was wondering if people could comment on the advantages and disadvantages of this procedure.
2) Since a monomer is a fragment and not a complete molecule, I "artificially" satisfied the valence by bonding it to other groups. I then set an intra-mcc to derive charges only for the relevant fragment. As I understand, this is in accordance with the R.E.D III tutorial (
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10). I was curious as to how the choice of the group selected to satisfy the valence will affect the partial charge.
eg. Let us say the polymer is (-CH2-)n. I derive partial charges for CH3-CH2-CH3 with intra-mcc on both CH3s. Would this provide accurate and useful partial charges? What factors would govern the choice of the chosen group (CH3 in this case)?
3) Regarding RBRA reorientation (
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3), I was wondering if the choice of the 3 atoms is arbitrary. In other words, can I choose any 3 atoms within my molecule for the reorientation procedure?
Thanks a lot for your help.
Regards,
Ganesh.
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Received on Sat Jul 11 2009 - 01:09:46 PDT
