Hi everyone,
I have been trying to create an isopeptide bond patch to join two monomers
of ubiquitin (Gly76->Lys48) using the amber force field (needed for GB), but
the result is that during minimization and dynamics, I have the following
output :
*--- Dynamics ---- step= 0 ---- time= 0 ---- delta_t= 0.001
--*
| E(kin)+E(poten)= -66.620 E(kin)= 0.689 temperature=
0.971 |
| E(poten)= -67.3086349 grad= 0.0000008 ANGL=
0.0000000 |
| BOND= 0.0000000 IMPR= 0.0000000 VDW+GBIN+GBSE=
-67.3086349 |
*------------------------------------------------------------------------------*
many potentials have value zero, whereas it is not zero without the patch.
(Deactivating GB does not change the problem)
I have pasted the patch in this mail, could someone tell me if something
looks suspicious in it ?
Thanks for your time,
Olivier Serve
topology
!!for amber forcefield not for standard xplor forcefield
presidue ISOP
group
modify atom -C charge = 0.5973 end
delete atom -OT1 end
delete atom -OT2 end
add atom -O type=O charge = -0.5679 end
add bond -C -O
ACCEPTOR -O -C
group
delete atom +HZ3 end
delete atom +HZ2 end
modify atom +NZ type=N charge = -0.3821 end
modify atom +HZ1 type=H charge = 0.2681 end
add bond -C +NZ
add angle -CA -C +NZ
add angle -O -C +NZ
add angle -C +NZ +CE
add angle -C +NZ +HZ1
ADD DIHEdral -C +NZ +CE +CD !triple
ADD DIHEdral -C +NZ +CE +CD !triple
ADD DIHEdral -C +NZ +CE +CD !triple
ADD DIHEdral -C +NZ +CE +HE1
ADD DIHEdral -C +NZ +CE +HE2
ADD DIHEdral -HA1 -CA -C +NZ
ADD DIHEdral -N -CA -C +NZ !triple
ADD DIHEdral -N -CA -C +NZ !triple
ADD DIHEdral -N -CA -C +NZ !triple
ADD DIHEdral -HA2 -CA -C +NZ
ADD DIHEdral -CA -C +NZ +HZ1
ADD DIHEdral -CA -C +NZ +CE
ADD DIHEdral -O -C +NZ +HZ1 ! double dihedral
ADD DIHEdral -O -C +NZ +HZ1 ! double dihedral
ADD DIHEdral -O -C +NZ +CE
ADD IMPROPER -C +CE +NZ +HZ1
ADD IMPROPER -CA +NZ -C -O
ADD IC -N -CA -C +NZ .0000 .00 180.00 .00 .0000
ADD IC -CA -C +NZ +CE .0000 .00 180.00 .00 .0000
ADD IC -C +NZ +CE +HE1 .0000 .00 180.00 .00 .0000
ADD IC +NZ -CA *-C -O .0000 .00 180.00 .00 .0000
ADD IC -C +CE *+NZ +HZ1 .0000 .00 180.00 .00 .0000
end
end
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