Hello,
I've put my comments below.
On Mon, Jul 19, 2010 at 2:04 PM, arikcohen <arikcohen.ucla.edu> wrote:
> 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
>
The paths are not needed. Also, why are you using leaprc.gaff from amber8
and leaprc.ff99SB from amber10? Just change these two lines to:
source leaprc.ff99SB
source leaprc.gaff
That should do it.
> loadamberprep DERACognateSub.prepin
>
> loadamberparams DERACognateSub.frcmod
>
> enzyme_design = loadpdb DERA_MonCogSub_NoH.1.pdb
>
Your unit name is now enzyme_design
>
> set enzyme_design head LYN.167.NZ
>
> set HPD tail HPD.252.C6
>
You do not need these. Furthermore, the the atom specification should be
"unit.residue#.atom". Your unit is enzyme_design, not the name of the
residue. In order to create a bond, just see the "bond" command in leap.
It seems that what you want is:
bond enzyme_design.167.NZ enzyme_design.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
>
I explained this error above, but again, this command is not needed
> >
> > 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.
>
This is pretty self-explanatory. This is almost certainly due to your
ligand having a non-integer charge. This is not close enough to an integer
to be round-off error (or something similar), so I would double-check your
charge derivation method for your ligand. If you need to redo it, consider
R.E.D. tools. There is a link to it on the amber website.
Hope this helps,
Jason
>
> I thank you in advance for your help
>
>
> Arik
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 19 2010 - 11:30:04 PDT
