[gmx-users] covalent binding- Improper Dih

[Emanuel Birru]

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..！>>. 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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