RE: [gmx-users] RE: RE: covalent binding- Improper Dih (Emanuel Birru)
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 CT9 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-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yongliang Yang Sent: Wednesday, 20 March 2013 2:14 PM To: gmx-users@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 CT9 0.0 1.60247 3 ; CT CT OS CT9 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 CT9 0.0 14.64400 2 ; JCC,7,(1986),230 CT S S CT9 0.0 2.51040 3 ; JCC,7,(1986),230 OS CT CT OS9 0.0 0.60250 3 ; parm98, TC,PC,PAK OS CT CT OS9 0.0 4.91620 2 ; Piotr et al. OS CT CT OH9 0.0 0.60250 3 ; parm98, TC,PC,PAK OS CT CT OH9 0.0 4.91620 2 ; parm98, TC,PC,PAK OH CT CT OH9 0.0 0.60250 3 ; parm98, TC,PC,PAK OH CT CT OH9 0.0 4.91620 2 ; parm98, TC,PC,PAK OH P OS CT9 0.0 1.04600 3 ; JCC,7,(1986),230 OH P OS CT9 0.0 5.02080 2 ; gg> ene.631g*/mp2 OS P OS CT9 0.0 1.04600 3 ; JCC,7,(1986),230 OS P OS CT9 0.0 5.02080 2 ; gg> ene.631g*/mp2 OS CT N* CK9 0.0 10.46000 1 ; parm98, TC,PC,PAK OS CT N* CM9 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 HC9 0.0 0.62760 3 ; Junmei et al, 1999 HC CT CT CT9 0.0 0.66944 3 ; Junmei et al, 1999 HC CT CM CM9 180.0 1.58992 3 ; Junmei et al, 1999 HC CT CM CM9 0.0 4.81160 1 ; Junmei et al, 1999 HO OH CT CT9 0.0 0.66944 3 ; Junmei et al, 1999 HO OH CT CT9 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 CT9 180.0 27.82360 2 ; Junmei et al, 1999 CT CM CM CT9 180.0 7.94960 1 ; Junmei et al, 1999 CT CT CT CT9 0.0 0.75312 3 ; Junmei et al, 1999 CT CT CT CT9 180.0 1.04600 2 ; Junmei et al, 1999 CT CT CT CT9 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 O
[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 CT9 0.0 1.60247 3 ; CT CT OS CT9 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 CT9 0.0 14.64400 2 ; JCC,7,(1986),230 CT S S CT9 0.0 2.51040 3 ; JCC,7,(1986),230 OS CT CT OS9 0.0 0.60250 3 ; parm98, TC,PC,PAK OS CT CT OS9 0.0 4.91620 2 ; Piotr et al. OS CT CT OH9 0.0 0.60250 3 ; parm98, TC,PC,PAK OS CT CT OH9 0.0 4.91620 2 ; parm98, TC,PC,PAK OH CT CT OH9 0.0 0.60250 3 ; parm98, TC,PC,PAK OH CT CT OH9 0.0 4.91620 2 ; parm98, TC,PC,PAK OH P OS CT9 0.0 1.04600 3 ; JCC,7,(1986),230 OH P OS CT9 0.0 5.02080 2 ; gg> ene.631g*/mp2 OS P OS CT9 0.0 1.04600 3 ; JCC,7,(1986),230 OS P OS CT9 0.0 5.02080 2 ; gg> ene.631g*/mp2 OS CT N* CK9 0.0 10.46000 1 ; parm98, TC,PC,PAK OS CT N* CM9 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 HC9 0.0 0.62760 3 ; Junmei et al, 1999 HC CT CT CT9 0.0 0.66944 3 ; Junmei et al, 1999 HC CT CM CM9 180.0 1.58992 3 ; Junmei et al, 1999 HC CT CM CM9 0.0 4.81160 1 ; Junmei et al, 1999 HO OH CT CT9 0.0 0.66944 3 ; Junmei et al, 1999 HO OH CT CT9 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 CT9 180.0 27.82360 2 ; Junmei et al, 1999 CT CM CM CT9 180.0 7.94960 1 ; Junmei et al, 1999 CT CT CT CT9 0.0 0.75312 3 ; Junmei et al, 1999 CT CT CT CT9 180.0 1.04600 2 ; Junmei et al, 1999 CT CT CT CT9 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 OS9 0.0 0.41840 3 ; Junmei et al, 1999 CT OS CT OS9 180.0 3.55640 2 ; Junmei et al, 1999 CT OS CT OS9 180.0 5.64840 1 ; Junmei et al, 1999 O C OS CT9 180.0 11.29680 2 ; Junmei et al, 1999 O C OS CT9 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 Cl9 180.0 1.88280 1 ; Junmei et al, 1999 Br CT CT Br9 0.0 0.0 0 ; Junmei et al, 1999 H1 CT CT OS9 0.0 1.04600 1 ; Junmei et al, 1999 H1 CT CT OH9 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 Cl9 0.0 1.04600 1 ; Junmei et al, 1999 H1 CT CT Br9 0.0 2.30120 1 ; Junmei et al, 1999 HC CT CT OS9 0.0 1.04600 1 ; Junmei et al, 1999 HC CT CT OH9 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 Cl9 0.0 1.04600 1 ; Ju
