AMBER Archive (2009)

Subject: [AMBER] R.E.D intra-mcc and reorientation

From: Ganesh Krishnan (hereisganesh_at_yahoo.com)
Date: Fri Jul 10 2009 - 17:00:35 CDT

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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