Dear Yun,
> From the references on webpage
> http://glycam.ccrc.uga.edu/ccrc/pages/cite.html, I did not find a
> comprehensive description of GLYCAM 04 force field. I really want to know
> the differences between GLYCAM 06 and GLYCAM04 in terms of application. So
> generally speaking, GLYCAM04 is more specific for carbohydrates while
> GLYCAM06 is more comprehensive for various types of organic molecules? Does
> it follow that for a system of protein and carbohydrate mixture, we should
> use either GLYCAM06 solely or, say, GLYCAM04 + ff99SB ?
A way to compare GLYCAM 2004 and GLYCAM 2006 is to use the "diff"
command applied to the two parameter sets. For sure, GLYCAM 2004
starts to be old. Thus, starting from the GLYCAM 2006 paper might be a
good bet.
diff $AMBERHOME/dat/leap/parm/Glycam_06f.dat
$AMBERHOME/dat/leap/parm/GLYCAM_06c.dat
Concerning GLYCAM 2006 I would like to underline that some force field
parameters are from time to time modified in the different versions of
GLYCAM 2006. We did not find any justification for these adaptations.
For instance, some dihedral parameters goes from 0.1 to 1.0 (or the
opposite I forgot) without any explanation. Why these corrections?
typos? improvements from where?
> In addition, I understand that GLYCAM04EP force field would better simulate
> a system with plenty of hydrogen bond interactions. But if I am just
> simulating a carbohydrate ligand with a protein receptor, would there be any
> benefit by using, say, GLYCAM04EP + ff99SB force fields?
Yun, here, I think you need to run & see, and build your own
experience. Try different parameter sets, run MD simulations and
follow key structural features/experimental data...
> What about glycam04EP.dat + parm99EP.dat? How much would be the increase in
> computational costs when we are accounting for these extra points?
Concerning extra-points, see:
http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1096-987X(199710)18:13%3C1632::AID-JCC5%3E3.0.CO;2-S/abstract
regards, Francois
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Received on Thu Sep 15 2011 - 01:00:03 PDT
