Dear Members,
I would be most thankful for any help in the following: I'm trying to
set up a covalent bond between my substrate and a catalytic lysine.
The tleap script is the following: (the substrate was named as HPD)
source /u/local/apps.old/amber8/serial/dat/leap/cmd/leaprc.gaff
source /u/local/apps/amber/10/dat/leap/cmd/leaprc.ff99SB
loadamberprep DERACognateSub.prepin
loadamberparams DERACognateSub.frcmod
enzyme_design = loadpdb DERA_MonCogSub_NoH.1.pdb
set enzyme_design head LYN.167.NZ
set HPD tail HPD.252.C6
check enzyme_design
charge enzyme_design
.
.
.
The output which I'm getting is the following:
>
> set enzyme_design head LYN.167.NZ
The value must be of the type: Atom
>
> set HPD tail HPD.252.C6
The value must be of the type: Atom
>
> check enzyme_design
Checking 'enzyme_design'....
ERROR: The unperturbed charge of the unit: -4.805188 is not integral.
WARNING: The unperturbed charge of the unit: -4.805188 is not zero.
I thank you in advance for your help
Arik
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Received on Mon Jul 19 2010 - 11:30:02 PDT
