Hi,
I get the following message several times when running leap on a file
which i am using to set up a simulation from an existing pdb struture.
I have my own parameters in a personalised parm file and wanted to
include water there too.
+---Tried to superimpose torsions for: *-H2-OW-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
I saw other people with similar errors who hadnt used the addAtomTypes
command, but as the excerpt from my file (below) shows i have done
this.
In my personalised parm file i have c6,c12,charge params along with
bond and angle values for HW&OW
is there someone who can see what i am doing wrong here?
Thanks,
Lorna
_____________________________________
>From my xleap command file:
> addAtomTypes {
> { "HW" "H" "sp3" }
> { "OW" "O" "sp3 "}
> }
h1 = createAtom H1 HW 0.417
h2 = createAtom H2 HW 0.417
ow = createAtom OW OW -0.834
set h1 element H
set h2 element H
set ow element O
r = createResidue WAT
add r h1
add r h2
add r ow
bond h1 ow
bond h2 ow
bond h1 h2
TP3 = createUnit TP3
add TP3 r
set TP3.1 restype solvent
set TP3.1 imagingAtom TP3.1.O
zMatrix TP3 {
{ H1 OW 0.9572 }
{ H2 OW H1 0.9572 104.52 }
}
WAT = TP3
addpdbatommap {
{ "HW1" "H1"}
{ "HW2" "H2"}
{ "OW" "OW" }
}
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Received on Tue Nov 22 2005 - 08:53:01 PST
