Dear Yun and Francois,
GLYCAM06 should be used instead of, and as a complete replacement for,
GLYCAM04. If you find anything that GLYCAM04 does significantly
better than GLYCAM06, you should certainly write us at
glycam.gmail.com and let us know about it.
Neither GLYCAM04 nor GLYCAM06 treat proteins. So, you need a protein
force field if you want to study a system containing both
carbohydrates and proteins. You also need a water force field (e.g.
TIP3P) if you want to include water.
Regarding subsequent releases of GLYCAM (c, d, e, f, g, etc.), see the
"Documents" column at glycam.org/params -- again, if you find anything
that changed and was not documented, please tell us. Omissions of
such information are not intentional. The notes in the documentation
might not be as detailed as a full paper would be, but they should
give you a good idea. You can always write us if you need more
information. I was unable to find a change between versions c and f
of GLYCAM06 to match your description. Could you be more specific?
We are developing a better versioning scheme. It should be live
within a few weeks. We'll also be updating the EP force field a bit
(for example, it uses some older-style nomenclature). If you want to
try an EP simulation, your life will be a lot easier if you wait for
that to happen.
In general, GLYCAM06 plus a good protein ff, say ff99SB, reproduces
hydrogen bonding pretty well. But, as Francois said, the best way to
determine which is better would be to try both. And, if you need very
detailed H-bonding information, you might need an EP force field.
And, yes, the additional points mean additional cost.
:-) Lachele
On Thu, Sep 15, 2011 at 3:54 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 15 2011 - 08:00:02 PDT
