eiichi tsuji wrote:
> i have some question about 'PATCH' statement.
> we have a small inhibitor covalently bound to our protein
> and would specify the attachment of the inhibitior to a
> cysteine residue.
> But i could not generate covalent bond between inhibitor
> and cysteine.
> i've prepared parameter and topology file for inhibitor,
> but are unsure of the 'PATCH' we need to specify the bonds.
> how do i generate covalent bond between inhibitor and protein?
You need to define a PRESidue which specifies what the linkage is. A
good place
to start is the disulfide patch from the tophcsdx.pro file:
PRESidue DISU { disulfide bridge ...CYS CYS...
\DISU/ }
GROUP
MODIfy ATOM 1CB CHARge= 0.19 END
MODIfy ATOM 1SG TYPE=S CHARge=-0.19 END
GROUP
MODIfy ATOM 2CB CHARge= 0.19 END
MODIfy ATOM 2SG TYPE=S CHARge=-0.19 END
ADD BOND 1SG 2SG
ADD ANGLe 1CB 1SG 2SG
ADD ANGLe 1SG 2SG 2CB
ADD DIHEdral 1CA 1CB 1SG 2SG
ADD DIHEdral 1CB 1SG 2SG 2CB
ADD DIHEdral 1SG 2SG 2CB 2CA
END {DISU}
So, the atoms from the first cysteine are prefixed by a "1" and from the
second by a "2"
(this is important for non-symmetric linkages such as the one you want).
Changing charges may be irrelevant for your purposes, but what you *do *
have to do is
to specify the new bond you create between the two residus and *all* of
the
bond angles (three atoms) and dihedral angles (four atoms) which
result. You may get
errors if you don't define these.
So you'll have lines like
ADD BOND 1SG 2O1 ! bond from Cys to inhibitor oxygen called O1
ADD ANGLE 1CB 1SG 2O1 ! angle across Cys sulfur
ADD ANGLE 1SG 2O1 2C2 ! angle from Cys sulfur, across inhibtor O1, to
next atom C2
A subsequent problem you might get would be that your inhibitor has
funny atoms in it,
where you've created new atom types -- you sometimes get OX1, CX2 atom
types after
using XPLO2D. The problem is, you need constants for the bonds and bond
angles
in your parameter file to take these into account!
If you are hooking up your Cys sulfur to a user-defined oxygen type
called OX1, you'd
have to add a new parameter file which includes lines something like
bond S OX1 2410.110 2.030 ! new bond between cys and inhibitor
oxygen
angle CH2E S OX1 599.823 103.800 ! angle between cys
beta-carbon, sulfur, and inhibitor atom
You would also need angle parameters for the angle between S, OX1, and
any atoms bound
to the OX1.
After these are all debugged, you can invoke a patch from generate like
the examples with
the disulfide, except your new patch residue will have some other name.
Hope this helped. Please feel free to ask for clairifications of this
hurried
explanation.
- Yoram
--
_______________________________________________________________________
Yoram A. Puius Albert Einstein College of Medicine
6th year M.D.-Ph.D. Department of Biochemistry
mailto:puius at aecom.yu.edu 1300 Morris Park Avenue, Bronx, NY 10461
http://www.geocities.com/Athens/Forum/7504
_______________________________________________________________________
