Dear Ismail,
> I want to perform organic solvent simulation using Amber. I built
> my test system dimethoxy ethane (CH3-O-CH2-CH2-O-CH3). I have tried
> to get the charges using RED-vIII.4. I tried a few conformations,
> then check the density with Amber and compare to the experimental
> density.
- For dimethoxy ethane, let's start with chemical equivalencing:
see
http://q4md-forcefieldtools.org/REDS/news.php
http://q4md-forcefieldtools.org/REDS/popup/popanteredtopequiv.php
Chemically equivalent atoms should bear the same charge values in MD
simulations. Ante_R.E.D. 1.x does not rigorously deal with chemical
equivalencing, while Ante_R.E.D. 2.0 in R.E.D. Server does.
In your case, Ante_R.E.D. 1.x will generate the following atom names
(in the first column of atom names in the P2N file format):
CT1 H1 H1 H1 O2 CT3 H3 H3 CT4 H4 H4 O5 CT6 H6 H6 H6
this has to be modify by hand
(see the tutorials .
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php)
Ante_R.E.D. 2.0 will generate:
CT1 H1 H1 H1 O2 CT3 H3 H3 CT3 H3 H3 O2 CT1 H1 H1 H1
that is correct
About the P2N file format, atom naming and chemical equivalencing see:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#ATOM-NAME
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#RULES
- You can find ethers in R.E.DD.B. as examples:
http://q4md-forcefieldtools.org/REDDB/download.php
Search project(s) by
-- R.E.DD.B. code (if known)
-- Molecule keyword x
-- Molecule name
-- Author lastname
-- Theory level/Basis set
Text Ether
Search... [Done]
Result(s) for search by Molecule keyword ether
Project name Methoxyethane
Project code W-17
etc...
http://q4md-forcefieldtools.org/REDDB/projects/W-17/
& corresponding RESP inputs:
http://q4md-forcefieldtools.org/REDDB/projects/W-17/input1.in
http://q4md-forcefieldtools.org/REDDB/projects/W-17/input2.in
(Obviously chemical equivalecing in 'methoxyethane' is different to
that in 'dimethoxy ethane')
> My questions are:
> (1) I include a few conformations with my calculation.
'Few' conformations is not accurate - a set of conformations is
involved in charge derivation - if the difference of energy between
the conformations, dE is 'small'; < 2-4 kcal/mol? Thus, in the Amber
FF, one or two conformations are often involved in charge derivation.
Please, see:
http://onlinelibrary.wiley.com/doi/10.1002/jcc.540161106/abstract
> Under certain set of conformations, the resulting charges are
> different for similar atoms. The molecule dimethoxy ethane is
> symmetic.
See chemical equivalencing above.
> Why does this happen? Is it OK to just average the charges out
> between similar atom?
'charge fitting' is not 'charge averaging':
- by charge fitting you involve multiple conformations (and multiple
orientations) to generate a single set of charge values
- by charge averaging you generate multiple sets of charge values
based on multiple conformations (taken individually) and you average
them to generate a single set of charge values.
> (2) Sometimes, when use more conformation, I get worse density
> value compare to experimental value. For example, I include just
> the gauche conformation at O-CH2-CH2-O and get density of 0.9000
> (experimental value is 0.8683). If I use the gauche and the trans
> conformation, I get 0.8900. I thought if I include more
> conformations like tTt, gTg, etc (the lower case is for the
> CH3-O-CH2-CH2) I get density ~0.8950, which is worse. Is this
> normal? I assume then it is safe if I use only the two conformation
> values?
'more' is vague once again; I would first try to select a conformation
that makes sense i. e. the lowest minimum or the two lowest minima.
etc...
- I would also try ESP charge derivation instead of RESP charge derivation.
- I would try the Connolly surface or the CHELPG algorithm in MEP
computation as well; please see:
http://q4md-forcefieldtools.org/REDS/popup/popkeyword.php
> (3) I don't quite get the REMARK REORIENT part. Does that part
> mean RESP is holding certain atoms constant with respect to certain
> axes?
The orientation of an optimized geometry affect MEP based charge
values. We observed a max. charge uncertainty of .07 e for a carbon
atom. See
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/#S7
The main idea with the rigid-body reorientation algorithm (RBRA)
implemented in the R.E.D. program is to derive reproducible charge
values independently of the QM program used (GAMESS, Firefly or
Gaussian) and independently of the initial orientation chosen by the
user. This is achieved by rigorously controlling the orientation of
the optimized geometry before MEP computation.
In general, we use pairs of molecular orientations; we select three
atoms in the RBRA algorithm, X Y Z to define a first orientation, and
then Z Y X in a second one to cancel out the effect of the first
orientation by the second one.
I hope this helps. Do not hesitate to ask for more information if
something is not clear. I forward this message in the Amber mailing
list as people there might be interested in this topic.
regards, Francois
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Aug 20 2011 - 01:30:03 PDT
