From: sarah k (dailycolors_at_gmail.com)
Date: Fri Dec 11 2009 - 01:32:10 CST

dear Yu Fang,

i mean after using QMTool (autogenerating coordinates and writing Gaussian
input file). and no, the geometry optimization, the single point calc or the
co-ordinate transformation aren't necessary. i didn't do them and i didn't
any errors.

specially if you're transferring your ligand to VMD after calculations and
processes from another softwares, don't do geometry optimization. it may
change your molecule. (i should admit I'm not professional so I'm not sure
about anything i say!!)

i used analog parameters to assign necessary values. for the error of
"expected floating-point number but got " others should help. i myself
received an application error saying it can't recognize the DEFAULTER
command. you'd better use analog parameters and be careful that even if one
parameter remain unassigned, it won't appear in parameter file and in
simulation you will receive errors.

if you have N N bonds or angles containing N N or some N N N diheadrals, you
can't find any parameter in analog lists. so i myself wrote down the number
of them the bond, angle or diheadral and added them to the final parameter
file manually.

that was all i knew. and i should thank for one of your questions. it helped
me fix another error.
Feel lucky,
Sarah