Dear Yun,
> As you said in the other email, I have to do validation no matter what kind
> of parameters I choose. So I think, at least, I need to validate with the
> conformational behavior of the per-OH-thiomethyl-Rhamnoside and the
> per-OH-O-methyl-Rhamnoside.
If this is _Your_ choice, ok.
From a charge fitting point of view, you might look at the errors
generated during the fitting step because of the use of the
constraints between the building blocks. You could also look at RRMS
value although it might not be an issue (See for instance:
http://www.sciencedirect.com/science/article/pii/S0010465511002086 ).
> But it seems that I need to build a disaccharide version for each case, so
> that I could look at average phi and psi dihedral angles, average distances
> between atoms on adjacent sugar rings, etc. But for the thiomethyl rhamnose,
> what I could find are some nOes between protons on different sugar rings of
> the S-disaccharide. So how to calculate normalized nOes from AMBER,
> according to different mixing time?
At a mixing time value, NOEs can be converted into distances (+/- ...;
these distances can be ploted versus the mixing time), and these
distances could be followed during MD. right? We used to do that
manually - NMR software do that automatically by now... I do not know
if the Amber suite has this feature.
> And as you noted in the other email, the assignment of atom types for the
> atom linking sugar part and amino acid part could be problematic. I think I
> will use glycam atom types for the sulfur atom and the methylene attached,
> since the validations would be with glycam force field (whether modified or
> not).
The atom type for the sulfur atom is identical in AMBER and GLYCAM.
The main atom type difference between AMBER and GLYCAM is CT versus CG
for the sp3 carbon atoms.
See
http://q4md-forcefieldtools.org/REDDB/projects/F-85/script1.ff
for instance a sugar fragment:
# The central fragment - allows polymerisation of per-OR a(1,4)Glc (R
= Me, Bn, Ac or Bz)
# MGR = loadmol2 1-MGR.mol2
MGR = loadmol2 tripos8.mol2
set MGR name "MGR"
set MGR head MGR.1.C4
set MGR tail MGR.1.O1
set MGR.1 connect0 MGR.1.C4
set MGR.1 connect1 MGR.1.O1
set MGR.1 restype saccharide
set MGR.1 name "MGR"
# set FF atom types
set MGR.1.C1 type CG
set MGR.1.H1 type H2
set MGR.1.O1 type OS
set MGR.1.C2 type CG
set MGR.1.H2 type H1
set MGR.1.C3 type CG
set MGR.1.H3 type H1
set MGR.1.C4 type CG
set MGR.1.H4 type H1
set MGR.1.C5 type CG
set MGR.1.H5 type H1
set MGR.1.O5 type OS
set MGR.1.C6 type CG
set MGR.1.H61 type H1
set MGR.1.H62 type H1
a peptide fragment:
# Succinamide fragment
# SCC = loadmol2 6-SCC.mol2
SCC = loadmol2 tripos13.mol2
set SCC name "SCC"
set SCC head SCC.1.N1
set SCC tail SCC.1.C4
set SCC.1 connect0 SCC.1.N1
set SCC.1 connect1 SCC.1.C4
set SCC.1 restype protein
set SCC.1 name "SCC"
# set FF atom types
set SCC.1.N1 type N
set SCC.1.H1 type H
set SCC.1.C1 type C
set SCC.1.O1 type O
set SCC.1.C2 type CT
set SCC.1.H21 type HC
set SCC.1.H22 type HC
set SCC.1.C3 type CT
set SCC.1.H31 type HC
set SCC.1.H32 type HC
set SCC.1.C4 type C
set SCC.1.O4 type O
> It seems that the validation of thioglycosidic parameters in my case would
> be very "indirect" using the S-disaccharide, but is there a better way?
I did not check the literature. You could follow QM data obtained
using high theory levels.
> By the way, I only have access to amber11, which did not come with glycam04
> data files, which although I can get from the glycam website. But how can I
> tell LEaP to use a specific data version such as Glycam_04k.dat (is this the
> one you used with amber10)?
I will ask here, and send you the GLYCAM 2004 parameter file we used.
Do not worry we also got lost between all these GLYCAM versions. The
parm94, parm96, parm98, parm99, 99SB etc... nomenclature is far more
simple/fully justified: one paper - one parameter file.
I am not sure you should use this GLYCAM 2004 parameter file in your
case (to be checked). Cyclodextrins are particular oligosaccharides as
they are cyclic (may be this is the main reason why GLYCAM 2006
display these limitations). In general, this is advised to use the
last version of a force field; although better double checking what
people suggest.
Personally, I would be interested in knowing if applying Amber scaling
factors for 1-4 non-bonding interactions to all your molecular system
works ;-)
regards, Francois
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Received on Wed Sep 21 2011 - 00:30:04 PDT
