[gmx-users] RE: RE: covalent binding- Improper Dih (Emanuel Birru)
Emanuel Birru
Emanuel.Birru at monash.edu
Wed Mar 20 07:16:00 CET 2013
Hi Jeremy,
I have checked how improper dihedral should look like in Amber, guessing that you used amber99sb force field. But I am wondering from where the improper in your ligand.itp was generated. As it doesn not look alike with the amber force field. It actually is not the problem of multiplicity but the number of parameters that you put in the improper is not enough. It should be at least three parameters in the improper section
Yours look like
[ impropers ]
CAD OAX CAB CAG 0.000 167.4 (two parameters here angle and force constant)
Whereas the program is looking for
CT CT OS CT 9 0.0 1.60247 3 (here function, angel, force constant and multiplicity??) copied from the amber bonded force field parameter :)
I think you should generate a logical itp file which fullfil all the necessary requirements before you run you simulation.
Cheers,
EB
-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yongliang Yang
Sent: Wednesday, 20 March 2013 2:14 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] RE: RE: covalent binding- Improper Dih (Emanuel Birru)
Dear Eb,
Thanks for the reply and input! I have posted part of the bonded itp file as below. Could you please be kind to specify how to revise the multiplicity? Many thanks! BTW, the force field we used is Amber. Thanks again!
Cheers
Jeremy
--------------------------
[ dihedraltypes ]
;i j k l func
CT CT OS CT 9 0.0 1.60247 3 ;
CT CT OS CT 9 180.0 0.41840 2 ;
C N CT C 9 0.0 1.12968 2 ; new for 99sb
C N CT C 9 0.0 1.75728 3 ; new for 99sb
N CT C N 9 180.0 1.88280 1 ; new for 99sb
N CT C N 9 180.0 6.61072 2 ; new for 99sb
N CT C N 9 180.0 2.30120 3 ; new for 99sb
CT CT N C 9 0.0 8.36800 1 ; new for 99sb
CT CT N C 9 0.0 8.36800 2 ; new for 99sb
CT CT N C 9 0.0 1.67360 3 ; new for 99sb
CT CT C N 9 0.0 0.83680 1 ; new for 99sb
CT CT C N 9 0.0 0.83680 2 ; new for 99sb
CT CT C N 9 0.0 1.67360 3 ; new for 99sb
H N C O 9 180.0 10.46000 2 ; JCC,7,(1986),230
H N C O 9 0.0 8.36800 1 ; J.C.cistrans-NMA DE
CT S S CT 9 0.0 14.64400 2 ; JCC,7,(1986),230
CT S S CT 9 0.0 2.51040 3 ; JCC,7,(1986),230
OS CT CT OS 9 0.0 0.60250 3 ; parm98, TC,PC,PAK
OS CT CT OS 9 0.0 4.91620 2 ; Piotr et al.
OS CT CT OH 9 0.0 0.60250 3 ; parm98, TC,PC,PAK
OS CT CT OH 9 0.0 4.91620 2 ; parm98, TC,PC,PAK
OH CT CT OH 9 0.0 0.60250 3 ; parm98, TC,PC,PAK
OH CT CT OH 9 0.0 4.91620 2 ; parm98, TC,PC,PAK
OH P OS CT 9 0.0 1.04600 3 ; JCC,7,(1986),230
OH P OS CT 9 0.0 5.02080 2 ; gg> ene.631g*/mp2
OS P OS CT 9 0.0 1.04600 3 ; JCC,7,(1986),230
OS P OS CT 9 0.0 5.02080 2 ; gg> ene.631g*/mp2
OS CT N* CK 9 0.0 10.46000 1 ; parm98, TC,PC,PAK
OS CT N* CM 9 0.0 10.46000 1 ; parm98, TC,PC,PAK
H1 CT C O 9 0.0 3.34720 1 ; Junmei et al, 1999
H1 CT C O 9 180.0 0.33472 3 ; Junmei et al, 1999
HC CT C O 9 0.0 3.34720 1 ; Junmei et al, 1999
HC CT C O 9 180.0 0.33472 3 ; Junmei et al, 1999
HC CT CT HC 9 0.0 0.62760 3 ; Junmei et al, 1999
HC CT CT CT 9 0.0 0.66944 3 ; Junmei et al, 1999
HC CT CM CM 9 180.0 1.58992 3 ; Junmei et al, 1999
HC CT CM CM 9 0.0 4.81160 1 ; Junmei et al, 1999
HO OH CT CT 9 0.0 0.66944 3 ; Junmei et al, 1999
HO OH CT CT 9 0.0 1.04600 1 ; Junmei et al, 1999
HO OH C O 9 180.0 9.62320 2 ; Junmei et al, 1999
HO OH C O 9 0.0 7.94960 1 ; Junmei et al, 1999
CM CM C O 9 180.0 9.10020 2 ; Junmei et al, 1999
CM CM C O 9 0.0 1.25520 3 ; Junmei et al, 1999
CT CM CM CT 9 180.0 27.82360 2 ; Junmei et al, 1999
CT CM CM CT 9 180.0 7.94960 1 ; Junmei et al, 1999
CT CT CT CT 9 0.0 0.75312 3 ; Junmei et al, 1999
CT CT CT CT 9 180.0 1.04600 2 ; Junmei et al, 1999
CT CT CT CT 9 180.0 0.83680 1 ; Junmei et al, 1999
CT CT OS C 9 0.0 1.60247 3 ; Junmei et al, 1999
CT CT OS C 9 180.0 3.34720 1 ; Junmei et al, 1999
CT OS CT OS 9 0.0 0.41840 3 ; Junmei et al, 1999
CT OS CT OS 9 180.0 3.55640 2 ; Junmei et al, 1999
CT OS CT OS 9 180.0 5.64840 1 ; Junmei et al, 1999
O C OS CT 9 180.0 11.29680 2 ; Junmei et al, 1999
O C OS CT 9 180.0 5.85760 1 ; Junmei et al, 1999
F CT CT F 9 180.0 5.02080 1 ; Junmei et al, 1999
Cl CT CT Cl 9 180.0 1.88280 1 ; Junmei et al, 1999
Br CT CT Br 9 0.0 0.00000 0 ; Junmei et al, 1999
H1 CT CT OS 9 0.0 1.04600 1 ; Junmei et al, 1999
H1 CT CT OH 9 0.0 1.04600 1 ; Junmei et al, 1999
H1 CT CT F 9 0.0 0.79496 1 ; Junmei et al, 1999
H1 CT CT Cl 9 0.0 1.04600 1 ; Junmei et al, 1999
H1 CT CT Br 9 0.0 2.30120 1 ; Junmei et al, 1999
HC CT CT OS 9 0.0 1.04600 1 ; Junmei et al, 1999
HC CT CT OH 9 0.0 1.04600 1 ; Junmei et al, 1999
HC CT CT F 9 0.0 0.79496 1 ; Junmei et al, 1999
HC CT CT Cl 9 0.0 1.04600 1 ; Junmei et al, 1999
HC CT CT Br 9 0.0 2.30120 1 ; Junmei et al, 1999
CT OS CT N* 9 0.0 1.60247 3 ; parm98.dat, TC,PC,PAK
CT OS CT N* 9 0.0 2.71960 2 ; Piotr et al.
X C C X 9 180.0 15.16700 2 ; Junmei et al, 1999
X C O X 9 180.0 11.71520 2 ; Junmei et al, 1999
X C OS X 9 180.0 11.29680 2 ; Junmei et al, 1999
X CA OH X 9 180.0 3.76560 2 ; Junmei et al, 99
X CM OS X 9 180.0 4.39320 2 ; Junmei et al, 1999
X C CA X 9 180.0 15.16700 2 ; intrpol.bsd.on C6H6
X C CB X 9 180.0 12.55200 2 ; intrpol.bsd.on C6H6
X C CM X 9 180.0 9.10020 2 ; intrpol.bsd.on C6H6
X C N* X 9 180.0 6.06680 2 ; JCC,7,(1986),230
X C NA X 9 180.0 5.64840 2 ; JCC,7,(1986),230
X C NC X 9 180.0 16.73600 2 ; JCC,7,(1986),230
X C OH X 9 180.0 9.62320 2 ; Junmei et al, 1999
X C CT X 9 0.0 0.00000 0 ; JCC,7,(1986),230
X CA CA X 9 180.0 15.16700 2 ; intrpol.bsd.on C6H6
X CA CB X 9 180.0 14.64400 2 ; intrpol.bsd.on C6H6
X CA CM X 9 180.0 10.66920 2 ; intrpol.bsd.on C6H6
X CA CT X 9 0.0 0.00000 0 ; JCC,7,(1986),230
X CA N2 X 9 180.0 10.04160 2 ; reinterpolated 93'
X CA NA X 9 180.0 6.27600 2 ; JCC,7,(1986),230
X CA NC X 9 180.0 20.08320 2 ; JCC,7,(1986),230
X CB CB X 9 180.0 22.80280 2 ; intrpol.bsd.on C6H6
X CB N* X 9 180.0 6.90360 2 ; JCC,7,(1986),230
X CB NB X 9 180.0 10.66920 2 ; JCC,7,(1986),230
X CB NC X 9 180.0 17.36360 2 ; JCC,7,(1986),230
X CK N* X 9 180.0 7.11280 2 ; JCC,7,(1986),230
X CK NB X 9 180.0 41.84000 2 ; JCC,7,(1986),230
X CM CM X 9 180.0 27.82360 2 ; intrpol.bsd.on C6H6
X CM CT X 9 0.0 0.00000 0 ; JCC,7,(1986),230
X CM N* X 9 180.0 7.74040 2 ; JCC,7,(1986),230
X CQ NC X 9 180.0 28.45120 2 ; JCC,7,(1986),230
X CT CT X 9 0.0 0.65084 3 ; JCC,7,(1986),230
X CT N X 9 0.0 0.00000 0 ; JCC,7,(1986),230
X CT N* X 9 0.0 0.00000 0 ; JCC,7,(1986),230
X CT N2 X 9 0.0 0.00000 0 ; JCC,7,(1986),230
X CT OH X 9 0.0 0.69733 3 ; JCC,7,(1986),230
X CT OS X 9 0.0 1.60387 3 ; JCC,7,(1986),230
X OH P X 9 0.0 1.04600 3 ; JCC,7,(1986),230
X OS P X 9 0.0 1.04600 3 ; JCC,7,(1986),230
X C N X 9 180.0 10.46000 2 ; AA,NMA
X CT N3 X 9 0.0 0.65084 3 ; JCC,7,(1986),230
X CT S X 9 0.0 1.39467 3 ; JCC,7,(1986),230
X CT SH X 9 0.0 1.04600 3 ; JCC,7,(1986),230
X C* CB X 9 180.0 7.00820 2 ; intrpol.bsd.onC6H6aa
X C* CT X 9 0.0 0.00000 0 ; JCC,7,(1986),230
X C* CW X 9 180.0 27.30060 2 ; intrpol.bsd.on C6H6
X CA CN X 9 180.0 15.16700 2 ; reinterpolated 93'
X CB CN X 9 180.0 12.55200 2 ; reinterpolated 93'
X CC CT X 9 0.0 0.00000 0 ; JCC,7,(1986),230
X CC CV X 9 180.0 21.54760 2 ; intrpol.bsd.on C6H6
X CC CW X 9 180.0 22.48900 2 ; intrpol.bsd.on C6H6
X CC NA X 9 180.0 5.85760 2 ; JCC,7,(1986),230
X CC NB X 9 180.0 10.04160 2 ; JCC,7,(1986),230
X CN NA X 9 180.0 6.38060 2 ; reinterpolated 93'
X CR NA X 9 180.0 9.72780 2 ; JCC,7,(1986),230
X CR NB X 9 180.0 20.92000 2 ; JCC,7,(1986),230
X CV NB X 9 180.0 10.04160 2 ; JCC,7,(1986),230
X CW NA X 9 180.0 6.27600 2 ; JCC,7,(1986),230
C C OA CH3 4 180.0 16.70000 2 ;
C C OA H 4 180.0 7.10000 2 ;
C C C CR1 4 180.0 5.90000 2 ;
C C C C 4 180.0 5.90000 2 ;
CH2 C C C 4 180.0 5.90000 2 ;
C CH2 C C 4 0.0 1.00000 6 ;
C C C CH2 4 180.0 5.90000 2 ;
CR1 C C C 4 180.0 5.90000 2 ;
CR1 C OA H 4 180.0 7.10000 2 ;
CR1 C OA CH3 4 180.0 16.70000 2 ;
-----------------------
Hi Jeremy,
It is hard to tell you what goes wrong from the information you gave us, but I suspect form the error message that the multiplicity that you used for the dihedral is wrong (the program is expecting 3 or 6 but you put 2 as multiplicity). Check it in the bonded itp file whether it is right.
If you put what kind of force field you use, give us you itp or top file and etc, it would be easy to trace the problem.
Cheers,
Eb
-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Yongliang Yang
Sent: Monday, 18 March 2013 4:44 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] covalent binding- Improper Dih
Dear Gromacs users,
We tried to simulate a protein-ligand covalent binding by Gromacs. The covalent bond was formed between a Cys and the Michael acceptor struture of the small molecule. We had generated a itp file for the small molecule by using PRODRG2 and converted it to rtp file. Unfortunately, the error message says: <<Fatal error ：Incorrect number of parameters - found 2, expected 3 or 6 for Improper Dih..ï¼ >>. We guess something was messed up in our rtp file. Could anybody be so kind to help? Part of the rtp file was posted below. Any input are welcomed. Many thanks!
Cheers
Jeremy Yang
<<ligand.rtp>>
--------------------------
[ impropers ]
CAD OAX CAB CAG 0.000 167.4
CAB CAD CAA HAB 0.000 167.4
CAG CAE OAY CAD 0.000 167.4
CAE CAG CAC HAE 0.000 167.4
CAC CAE CAA HAC 0.000 167.4
CAA CAF CAC CAB 0.000 167.4
CAM CAQ OAW CAH 0.000 167.4
CAT CAQ OAV CAU 0.000 167.4
CAN CAO CAK CAL 0.000 167.4
CAL CAN CAJ HAL 0.000 167.4
CAK CAN CAI HAK 0.000 167.4
CAI CAK CAS HAI 0.000 167.4
CAS CAI OAZ CAJ 0.000 167.4
CAJ CAL OBA CAS 0.000 167.4
CAN CAL CAJ CAS 0.000 209.3
CAL CAJ CAS CAI 0.000 209.3
CAJ CAS CAI CAK 0.000 209.3
CAS CAI CAK CAN 0.000 209.3
CAI CAK CAN CAL 0.000 209.3
CAK CAN CAL CAJ 0.000 209.3
CAD CAB CAA CAC 0.000 209.3
CAB CAA CAC CAE 0.000 209.3
CAA CAC CAE CAG 0.000 209.3
CAC CAE CAG CAD 0.000 209.3
CAE CAG CAD CAB 0.000 209.3
CAG CAD CAB CAA 0.000 209.3
[ dihedrals ]
CAG CAD OAX CAP 180.000 16.7 2
CAD CAG OAY HAY 180.000 7.1 2
CAH CAF CAA CAB 180.000 5.9 2
CAM CAH CAF CAA 180.000 5.9 2
CAQ CAM CAH CAF 180.000 5.9 2
CAT CAQ CAM CAH 0.000 1.0 6
CAM CAQ CAT CAU 0.000 1.0 6
CAO CAU CAT CAQ 180.000 5.9 2
CAN CAO CAU CAT 180.000 5.9 2
CAK CAN CAO CAU 180.000 5.9 2
CAI CAS OAZ HAZ 180.000 7.1 2
CAL CAJ OBA CAR 180.000 16.7 2
--
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