help on building PATCH

From: Matteo Pappalardo (mpappala_at_unict.it)
Date: Fri Jun 08 2012 - 03:15:53 CDT

Dear all,
I want to launch MD of MAO-B covalent bounded to its co-factor FAD. I
successfully parametrized FAD and simulated no-covalent bound
MAO-B/FAD system, as a test. In order to parametrize covalent bond i
try to use a PATCH during the generation of psf (i used disulfide
bridge patch as a template). Now i am encounetered a stop because my
patch do not bound the two molecules, and do not delete HG atom of the
cysteine involved into bond with FAD. here the simplified patch adopted
!MASS 1 c3 12.010000

PRESI FAD 0.6000
GROUP
ATOM CB CT2 -0.10 !
ATOM SG S -0.08 !
GROUP
ATOM C47 c3 0.019000
ATOM C48 c3 0.019800
ATOM C46 c3 0.019800
DELETE ATOM 1HG1
DELETE ATOM H29
DELETE ATOM C52
DELETE ATOM H30
DELETE ATOM H28
BOND C47 SG

while script used for generating psf is
package require psfgen
topology PATCH_FAD.rtf
topology FADalone.acpype/FADalone_CHARMM.rtf
topology /usr/local/lib/vmd/plugins/noarch/tcl/readcharmmtop1.1/top_all27_pro$
segment A {pdb mao1.pdb }
segment B {pdb fad1.pdb }
patch FAD B:1 A:297
coordpdb mao1.pdb A
coordpdb fad1.pdb B
guesscoord
writepsf mao-fad.psf
writepdb mao-fad.pdb

Can anyone help me?
best regards
Matteo

----------------------------------------------
Matteo Pappalardo, PhD
Chemical Science Department
University of Catania
Viale A. Doria 6 - I-95125 Catania ITALY
e-mail: mpappala_at_unict.it

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