Dear all:
I want to imitate the tutorial A2 to do the QM/MM simulation
with the water model replaced by amoeba. Then I do as follows:
leapin
xleap -s -f
NMA = loadpdb NMA_skeleton.pdb
edit NMA (do the relax)
solvatebox NMA TIP3PBOX 15
savepdb NMA NMA_slv.pdb
saveamberparm NMA NMA_slv.top NMA_slv.crd(save to see the box
information)
quit
Then:
pdbxyz NMA_slv
the NMA_slv.key:
parameters /home/fjliu/software/tinker/params/amoebabio09
a-axis 40.18
b-axis 39.30
c-axis 39.56
I get the NMA_slv.xyz. Followed by: analyze NMA_slv PC >
NMA_slv.analout, I got the error message:
Undefined Torsional Parameters :
Type Atom Names Atom
Classes
Torsion 1-C 2-C 7-N 8-C 40 3
1 40
MECHANIC -- Some Required Potential Energy Parameters are
Undefined
TINKER is Unable to Continue; Terminating the Current Calculation
What is wrong with it? Also I do the example in
/home/fjliu/software/amber14/src/pmemd.amoeba/build_amoeba/examples/JAC,thre
is no problem with the given jac.pdb. But if I extracted a water
molecule to do the pdbxyz, the atom type information will not give out,
then it will be wrong when I do the analyze.
Another question is can I do the QM/MM calculation with amoeba
water model? Thanks for your help!Fengjiao
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 10 2015 - 02:00:03 PDT
