Hi,
> Iam beginnig to develop parameters for a set of molecules and I will
> use R.E.D. to derive the charges. Why in the tutorial
> dimethylalaninedipeptide is divided into 3prtions.
I am not sure I understand what you mean: Do you mean the following sections?
-I.3.2.1- Single-conformation single-orientation RESP fits for new
dipeptide molecules
-I.3.2.2- Single- or multi-conformation multi-orientation RESP fits
for new dipeptide molecules
-I.3.2.3- Single- or multi-conformation multi-orientation RESP fits
for the central fragment of new amino-acids
-I.3.2.4- Multi-molecule multi-conformation multi-orientation RESP
fits for terminal fragments of new amino-acids
Here different approaches for charge derivation (for a whole molecule
and/or for molecular fragments using a defined set of molecular
orientations and conformations) are described.
> Can't we just derive charges for the whole molecule.
You have to select the approach corresponding to your need.
> I will derive the charges for carboxylic acid as well and Iam
> confused whether I should keep it as awhole molecule or divide it.
If you want to derive charges for a whole molecule or for a molecular
fragment you always use whole molecule(s). The fragment(s) are
designed during the charge fit using specific charge constraint(s).
You can find an example of charge derivation in R.E.DD.B. for ethanoic acid
http://q4md-forcefieldtools.org/REDDB/projects/W-34/
regards, Francois
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Received on Wed Nov 03 2010 - 00:00:02 PDT
