Yun
> I looked through the tutorial, but still not sure about which set of atoms
> to select for REORIENT, although I can get a vague idea from
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
If you run Ante_R.E.D. 2.0 the program will select a set of atoms for you.
You can select the atoms you wish - the idea is only to provide to the
user a way to control the molecular orientations of the optimized
geometry... then, you can find your own rules; select only heavy
atoms; or atoms belonging to a family of residues, etc...
the only restriction is that you should not select 3 linear atoms
see
http://q4md-forcefieldtools.org/REDDB/error.php
"Corrections carried out the October 4th, 2010 (Paris time)"
> I looked at the leap script provided and still not clear. So after I got
> RESP charges for the thio sugar, how do I set other parameters since it is
> not a standard module in any force field? Use antechamber with GAFF force
> field? Manually create a .frcmod file?
We generated the frcmod file by hand. If you run LEaP it will list the
missing force field parameters... So after having the listing of
missing force field parameters you can easily create your own frcmod
file by selecting the force field parameters you really want.
> Especially how to specify bond, angle, dihedral parameters for the linkage
> once I linked this thio sugar with another standard sugar (with GLYCAM
> parameters)? Adding something in the building block as GLYCAM and 99SB do?
Bonds and angles are generally not a problem; we get the constants by
analogy to another existing one. Equilibrium values are obtained by
geometry optimization by QM by using a large basis set or from X-ray
structures (CSD). Key dihedrals are recomputed. For instance, you
might need to develop new dihedral force field parameters for the
thio-rhamnoside linkage...
regards, Francois
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Received on Sat Aug 27 2011 - 00:00:03 PDT
