Dear Mithun Biswas,
> I am trying to derive partial charges for a ligand covalently bonded to
> DNA. I guess one would need to cap the DNA ends for the charge fitting
> procedure. What are capping residues for DNA/RNA ? Are they the same
> ACE/NME residues as used for peptides ? Thanks.
if you run "tleap -f leaprc.ff99SB"
then you execute the following commands:
charge DC ---> total charge = -1
charge DC3
charge DC5 ---> sum(DC3+DC5) = -1
charge ALA ---> total charge = 0
charge NALA ---> total charge = +1
charge CALA ---> total charge = -1
-> this means the total charge values of a molecular fragment or the
sum of two fragments takes an integer value.
Thus, you have to keep these rules in mind when you wish to develop a
new molecular fragment.
ACE & NME capping groups are used for splitting a peptide bond in two
building blocks. Nucleotide fragments are generally constructed
between and an alkyl-ether or ester function and an alcohol setting
the total charge of the two corresponding chemical groups to zero
using inter-molecular charge constraint(s) during the charge fitting
step.
See
http://onlinelibrary.wiley.com/doi/10.1002/jcc.540161106/abstract
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/
You can find many tutorials about fragment buildings at
http://q4md-forcefieldtools.org/Tutorial/
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
You can information about constraints in charge fitting at:
http://q4md-forcefieldtools.org/RED/resp/
regards, Francois
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Received on Fri May 25 2012 - 00:00:03 PDT
