Re: [gmx-users] Re: adding ff parameter of modified residue to charmm ff
My way of doing it is: (1) add two new residues entries (with two different names) for glycine and seine in the rtp file and corresponding FF files. The new entries in the rtp file for glycine and serine should have the same number of atoms as in the real molecule (delete the unnecessary H or OH groups if needed) (2) then use pdb2gmx (3) then manually construct the bond, angle and dihedrals at the linkage site. Cheers, Jianguo From: bharat gupta bharat.85.m...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, 3 March 2011 11:31:38 Subject: [gmx-users] Re: adding ff parameter of modified residue to charmm ff Hi, I followed the tutorial - http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field for updating the Charmm FF for my modified residue .. I added the residues to the .rtp file , then I added the new atom types in .atp file , The compound has some linkage with serine and glycine ... I want to know how and where shall I add the linkage parameters and the parameters (in bits) given below (The parameter file of the compound looks like this ) .. BONDS ! !V(bond) = Kb(b - b0)**2 ! !Kb: kcal/mole/A**2 !b0: A ! !atom type Kb b0 CA1 CA2 305.00 1.3750 ! CA2 CA3 305.00 1.3750 ! CA3 CA4 305.00 1.3750 ! HPc CA1 340.000 1.08 ! HPc CA2 340.000 1.08 ! HPc CA3 340.000 1.08 ! HPc CA4 340.000 1.08 ! ANGLES ! !V(angle) = Ktheta(Theta - Theta0)**2 ! !V(Urey-Bradley) = Kub(S - S0)**2 ! !Ktheta: kcal/mole/rad**2 !Theta0: degrees !Kub: kcal/mole/A**2 (Urey-Bradley) !S0: A ! !atom types KthetaTheta0 Kub S0 ! NR2c CP2c NR1c 130.00114.00 ! CP2c NR2c CP1c 130.00106.00 ! CP2c NR1c CP1c 130.00107.90 ! NR2c CP1c CP1c 130.00108.30 ! NR2c CP1c CE1c 45.80129.50 ! NR1c CP1c OcH42.00126.00 ! NR1c CP1c CP1c 130.00103.00 ! !Connection to the ser fragment !-- CT2 CT1 CP2c52.000 108. ! ALLOW ALI PEP POL ARO HB CT1 CP2c 50.000 109.5000 ! ALLOW PEP NH1 CT1 CP2c 50.000 107. ! ALLOW PEP POL ARO ALI NR2C CP2C CT1 40.00125.00 ! !Connection to the gly fragment !-- NR1C CT2 C 50.000 107. NR1c CT2 HB 48.000 108. CP2C NR1C CT2 36.00129.00 CP1C NR1C CT2 32.00123.40 ! DIHEDRALS ! !V(dihedral) = Kchi(1 + cos(n(chi) - delta)) ! !Kchi: kcal/mole !n: multiplicity !delta: degrees ! !atom types Kchin delta ! CP2C NR2C CP1C CP1C14. 2 180.00 ! CP2C NR1C CP1C CP1C14. 2 180.00 ! NR2C CP2C NR1C CP1C14. 2 180.00 ! NR2C CP1C CP1C NR1C 4. 2 180.00 ! NR1C CP2C NR2C CP1C 4. 2 180.00 ! CA1 CA2 CA3 CA4 3.1000 2 180.00 ! !barrier CA-CB CP1C CP1C CE1C HA1C 6.84 2 180.00 ! CP1C CP1C CE1C CA1 6.84 2 180.00 ! NR2C CP1C CE1C HA1C 6.84 2 180.00 ! NR2C CP1C CE1C CA1 6.84 2 180.00 ! ! !barrier CB-CG2 CP1C CE1C CA1 CA2 1.4 2 180.00 ! HA1C CE1C CA1 CA2 1.4 2 180.00 ! ! CP2C NR1C CP1C OCH 14.002 180.00 ! NR2C CP2C NR1C CT2 14.002 180.00 ! NR2C CP1C CP1C OCH 14.002 180.00 ! CP1C NR1C CP2C CT1 14.002 180.00 ! OCH CP1C NR1C CT2 14.002 180.00 ! CP1C NR2C CP2C CT1 14.002 180.00 ! CP1C CP1C NR1C CT2 14.002 180.00 ! CT1 CP2C NR1C CT2 14.002 180.00 ! ! ! Linking the chromophore and the glycine fragment OCCT2 NR1C 0. 1 0.00 ! NH1 CCT2 NR1c 0.6000 1 0.00 ! CP2C NR1C CT2 HB 0.032 3 0.00 ! CP2c NR1c CT2 C 0.032 3 0.00 ! CP1c NR1c CT2 HB 0.032 3 180.00 ! CP1c NR1c CT2 C 0.032 3 180.00 ! ! ! Linking the chromophore and the serine fragment CNH1 CT1 CP2C 0.2000 1 180.00 ! HNH1 CT1 CP2C 0. 1 0.00 ! NR2C CP2C CT1 HB 0.105 3 180.00 ! NR2C CP2C CT1 NH10.105 3 180.00 ! NR2C CP2C CT1 CT20.105 3 180.00 ! NR1C CP2C CT1 HB 0.105 3 0.00 ! IMPROPER ! !V(improper) = Kpsi(psi - psi0)**2 ! !Kpsi: kcal/mole/rad**2 !psi0: degrees !note that the second column of numbers (0) is ignored ! !atom types Kpsi psi0 ! CP2C NR2C NR1C CT1 0.5 0 0.00 CP2C NR1C NR2C CT1 0.5 0 0.00 ! CP1C NR1C CP1C OCH 0.5 0 0.00 CP1C CP1C NR1C OCH 0.5 0 0.00 ! NR1C CP1C CP2C CT2 0.45 0 0.00 NR1C CP2C CP1C CT2 0.45 0 0.00 ! CP1C NR2C CP1C CE1C 220.0 0 0.00 CP1C CP1C NR2C CE1C 220.0 0 0.00 ! !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] ! !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) !Rmin/2: A, Rmin,i,j = Rmin
Re: [gmx-users] Re: adding ff parameter of modified residue to charmm ff
but I have the torsion angles , bond angles for my residue .. The problem is I don't know which one to put where as the charmm FF parameter that I have got doesnot match with the charmm ff parameter in gromacs.. that's y I am confused .. On Thu, Mar 3, 2011 at 12:58 AM, Jianguo Li ljg...@yahoo.com.sg wrote: My way of doing it is: (1) add two new residues entries (with two different names) for glycine and seine in the rtp file and corresponding FF files. The new entries in the rtp file for glycine and serine should have the same number of atoms as in the real molecule (delete the unnecessary H or OH groups if needed) (2) then use pdb2gmx (3) then manually construct the bond, angle and dihedrals at the linkage site. Cheers, Jianguo -- *From:* bharat gupta bharat.85.m...@gmail.com *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thursday, 3 March 2011 11:31:38 *Subject:* [gmx-users] Re: adding ff parameter of modified residue to charmm ff Hi, I followed the tutorial - http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field for updating the Charmm FF for my modified residue .. I added the residues to the .rtp file , then I added the new atom types in .atp file , The compound has some linkage with serine and glycine ... I want to know how and where shall I add the linkage parameters and the parameters (in bits) given below (The parameter file of the compound looks like this ) .. BONDS ! !V(bond) = Kb(b - b0)**2 ! !Kb: kcal/mole/A**2 !b0: A ! !atom type Kb b0 CA1 CA2 305.00 1.3750 ! CA2 CA3 305.00 1.3750 ! CA3 CA4 305.00 1.3750 ! HPc CA1 340.000 1.08 ! HPc CA2 340.000 1.08 ! HPc CA3 340.000 1.08 ! HPc CA4 340.000 1.08 ! ANGLES ! !V(angle) = Ktheta(Theta - Theta0)**2 ! !V(Urey-Bradley) = Kub(S - S0)**2 ! !Ktheta: kcal/mole/rad**2 !Theta0: degrees !Kub: kcal/mole/A**2 (Urey-Bradley) !S0: A ! !atom types KthetaTheta0 Kub S0 ! NR2c CP2c NR1c 130.00114.00 ! CP2c NR2c CP1c 130.00106.00 ! CP2c NR1c CP1c 130.00107.90 ! NR2c CP1c CP1c 130.00108.30 ! NR2c CP1c CE1c 45.80129.50 ! NR1c CP1c OcH42.00126.00 ! NR1c CP1c CP1c 130.00103.00 ! !Connection to the ser fragment !-- CT2 CT1 CP2c52.000 108. ! ALLOW ALI PEP POL ARO HB CT1 CP2c 50.000 109.5000 ! ALLOW PEP NH1 CT1 CP2c 50.000 107. ! ALLOW PEP POL ARO ALI NR2C CP2C CT1 40.00125.00 ! !Connection to the gly fragment !-- NR1C CT2 C 50.000 107. NR1c CT2 HB 48.000 108. CP2C NR1C CT2 36.00129.00 CP1C NR1C CT2 32.00123.40 ! DIHEDRALS ! !V(dihedral) = Kchi(1 + cos(n(chi) - delta)) ! !Kchi: kcal/mole !n: multiplicity !delta: degrees ! !atom types Kchin delta ! CP2C NR2C CP1C CP1C14. 2 180.00 ! CP2C NR1C CP1C CP1C14. 2 180.00 ! NR2C CP2C NR1C CP1C14. 2 180.00 ! NR2C CP1C CP1C NR1C 4. 2 180.00 ! NR1C CP2C NR2C CP1C 4. 2 180.00 ! CA1 CA2 CA3 CA4 3.1000 2 180.00 ! !barrier CA-CB CP1C CP1C CE1C HA1C 6.84 2 180.00 ! CP1C CP1C CE1C CA1 6.84 2 180.00 ! NR2C CP1C CE1C HA1C 6.84 2 180.00 ! NR2C CP1C CE1C CA1 6.84 2 180.00 ! ! !barrier CB-CG2 CP1C CE1C CA1 CA2 1.4 2 180.00 ! HA1C CE1C CA1 CA2 1.4 2 180.00 ! ! CP2C NR1C CP1C OCH 14.002 180.00 ! NR2C CP2C NR1C CT2 14.002 180.00 ! NR2C CP1C CP1C OCH 14.002 180.00 ! CP1C NR1C CP2C CT1 14.002 180.00 ! OCH CP1C NR1C CT2 14.002 180.00 ! CP1C NR2C CP2C CT1 14.002 180.00 ! CP1C CP1C NR1C CT2 14.002 180.00 ! CT1 CP2C NR1C CT2 14.002 180.00 ! ! ! Linking the chromophore and the glycine fragment OCCT2 NR1C 0. 1 0.00 ! NH1 CCT2 NR1c 0.6000 1 0.00 ! CP2C NR1C CT2 HB 0.032 3 0.00 ! CP2c NR1c CT2 C 0.032 3 0.00 ! CP1c NR1c CT2 HB 0.032 3 180.00 ! CP1c NR1c CT2 C 0.032 3 180.00 ! ! ! Linking the chromophore and the serine fragment CNH1 CT1 CP2C 0.2000 1 180.00 ! HNH1 CT1 CP2C 0. 1 0.00 ! NR2C CP2C CT1 HB 0.105 3 180.00 ! NR2C CP2C CT1 NH10.105 3 180.00 ! NR2C CP2C CT1 CT20.105 3 180.00 ! NR1C CP2C CT1 HB 0.105 3 0.00 ! IMPROPER ! !V(improper) = Kpsi(psi - psi0)**2 ! !Kpsi: kcal/mole/rad**2 !psi0: degrees !note that the second column of numbers (0) is ignored ! !atom types Kpsi psi0 ! CP2C NR2C NR1C CT1 0.5 0 0.00 CP2C NR1C NR2C CT1 0.5 0 0.00 ! CP1C NR1C CP1C OCH 0.5 0 0.00 CP1C CP1C
Re: [gmx-users] Re: adding ff parameter of modified residue to charmm ff
On 03/03/11, bharat gupta bharat.85.m...@gmail.com wrote: Hi, I followed the tutorial - http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field for updating the Charmm FF for my modified residue .. I added the residues to the .rtp file , then I added the new atom types in .atp file , The compound has some linkage with serine and glycine ... I want to know how and where shall I add the linkage parameters and the parameters (in bits) given below Without some idea what you mean by linkage with serine and glycine it's too hard to offer help. Mark (The parameter file of the compound looks like this ) .. BONDS ! !V(bond) = Kb(b - b0)**2 ! !Kb: kcal/mole/A**2 !b0: A ! !atom type Kb b0 CA1 CA2 305.00 1.3750 ! CA2 CA3 305.00 1.3750 ! CA3 CA4 305.00 1.3750 ! HPc CA1 340.000 1.08 ! HPc CA2 340.000 1.08 ! HPc CA3 340.000 1.08 ! HPc CA4 340.000 1.08 ! ANGLES ! !V(angle) = Ktheta(Theta - Theta0)**2 ! !V(Urey-Bradley) = Kub(S - S0)**2 ! !Ktheta: kcal/mole/rad**2 !Theta0: degrees !Kub: kcal/mole/A**2 (Urey-Bradley) !S0: A ! !atom types Ktheta Theta0 Kub S0 ! NR2c CP2c NR1c 130.00 114.00 ! CP2c NR2c CP1c 130.00 106.00 ! CP2c NR1c CP1c 130.00 107.90 ! NR2c CP1c CP1c 130.00 108.30 ! NR2c CP1c CE1c 45.80 129.50 ! NR1c CP1c OcH 42.00 126.00 ! NR1c CP1c CP1c 130.00 103.00 ! !Connection to the ser fragment !-- CT2 CT1 CP2c 52.000 108. ! ALLOW ALI PEP POL ARO HB CT1 CP2c 50.000 109.5000 ! ALLOW PEP NH1 CT1 CP2c 50.000 107. ! ALLOW PEP POL ARO ALI NR2C CP2C CT1 40.00 125.00 ! !Connection to the gly fragment !-- NR1C CT2 C 50.000 107. NR1c CT2 HB 48.000 108. CP2C NR1C CT2 36.00 129.00 CP1C NR1C CT2 32.00 123.40 ! DIHEDRALS ! !V(dihedral) = Kchi(1 + cos(n(chi) - delta)) ! !Kchi: kcal/mole !n: multiplicity !delta: degrees ! !atom types Kchi n delta ! CP2C NR2C CP1C CP1C 14. 2 180.00 ! CP2C NR1C CP1C CP1C 14. 2 180.00 ! NR2C CP2C NR1C CP1C 14. 2 180.00 ! NR2C CP1C CP1C NR1C 4. 2 180.00 ! NR1C CP2C NR2C CP1C 4. 2 180.00 ! CA1 CA2 CA3 CA4 3.1000 2 180.00 ! !barrier CA-CB CP1C CP1C CE1C HA1C 6.84 2 180.00 ! CP1C CP1C CE1C CA1 6.84 2 180.00 ! NR2C CP1C CE1C HA1C 6.84 2 180.00 ! NR2C CP1C CE1C CA1 6.84 2 180.00 ! ! !barrier CB-CG2 CP1C CE1C CA1 CA2 1.4 2 180.00 ! HA1C CE1C CA1 CA2 1.4 2 180.00 ! ! CP2C NR1C CP1C OCH 14.00 2 180.00 ! NR2C CP2C NR1C CT2 14.00 2 180.00 ! NR2C CP1C CP1C OCH 14.00 2 180.00 ! CP1C NR1C CP2C CT1 14.00 2 180.00 ! OCH CP1C NR1C CT2 14.00 2 180.00 ! CP1C NR2C CP2C CT1 14.00 2 180.00 ! CP1C CP1C NR1C CT2 14.00 2 180.00 ! CT1 CP2C NR1C CT2 14.00 2 180.00 ! ! ! Linking the chromophore and the glycine fragment O C CT2 NR1C 0. 1 0.00 ! NH1 C CT2 NR1c 0.6000 1 0.00 ! CP2C NR1C CT2 HB 0.032 3 0.00 ! CP2c NR1c CT2 C 0.032 3 0.00 ! CP1c NR1c CT2 HB 0.032 3 180.00 ! CP1c NR1c CT2 C 0.032 3 180.00 ! ! ! Linking the chromophore and the serine fragment C NH1 CT1 CP2C 0.2000 1 180.00 ! H NH1 CT1 CP2C 0. 1 0.00 ! NR2C CP2C CT1 HB 0.105 3 180.00 ! NR2C CP2C CT1 NH1 0.105 3 180.00 ! NR2C CP2C CT1 CT2 0.105 3 180.00 ! NR1C CP2C CT1 HB 0.105 3 0.00 ! IMPROPER ! !V(improper) = Kpsi(psi - psi0)**2 ! !Kpsi: kcal/mole/rad**2 !psi0: degrees !note that the second column of numbers (0) is ignored ! !atom types Kpsi psi0 ! CP2C NR2C NR1C CT1 0.5 0 0.00 CP2C NR1C NR2C CT1 0.5 0 0.00 ! CP1C NR1C CP1C OCH 0.5 0 0.00 CP1C CP1C NR1C OCH 0.5 0 0.00 ! NR1C CP1C CP2C CT2 0.45 0 0.00 NR1C CP2C CP1C CT2 0.45 0 0.00 ! CP1C NR2C CP1C CE1C 220.0 0 0.00 CP1C CP1C NR2C CE1C 220.0 0 0.00 ! !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] ! !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j ! !atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 ! !CAc 5.00 -0.07 1.992400 ! ALLOW ARO ! ! benzene (JES) CA1 5.00 -0.07 1.992400 ! ALLOW ARO CA2
Re: [gmx-users] Re: adding ff parameter of modified residue to charmm ff
The residue is a chromophore of Green Fluorescent Protein. The parameter file that I have got has the connection for serine and glycine :- !Connection to the ser fragment !-- CT2 CT1 CP2c52.000 108. ! ALLOW ALI PEP POL ARO HB CT1 CP2c 50.000 109.5000 ! ALLOW PEP NH1 CT1 CP2c 50.000 107. ! ALLOW PEP POL ARO ALI NR2C CP2C CT1 40.00125.00 ! NR1C CP2C CT1 35.00121.40 ! ! !Connection to the gly fragment !-- NR1C CT2 C 50.000 107. NR1c CT2 HB 48.000 108. CP2C NR1C CT2 36.00129.00 CP1C NR1C CT2 32.00123.40 On Thu, Mar 3, 2011 at 1:23 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 03/03/11, *bharat gupta * bharat.85.m...@gmail.com wrote: Hi, I followed the tutorial - http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field for updating the Charmm FF for my modified residue .. I added the residues to the .rtp file , then I added the new atom types in .atp file , The compound has some linkage with serine and glycine ... I want to know how and where shall I add the linkage parameters and the parameters (in bits) given below Without some idea what you mean by linkage with serine and glycine it's too hard to offer help. Mark (The parameter file of the compound looks like this ) .. BONDS ! !V(bond) = Kb(b - b0)**2 ! !Kb: kcal/mole/A**2 !b0: A ! !atom type Kb b0 CA1 CA2 305.00 1.3750 ! CA2 CA3 305.00 1.3750 ! CA3 CA4 305.00 1.3750 ! HPc CA1 340.000 1.08 ! HPc CA2 340.000 1.08 ! HPc CA3 340.000 1.08 ! HPc CA4 340.000 1.08 ! ANGLES ! !V(angle) = Ktheta(Theta - Theta0)**2 ! !V(Urey-Bradley) = Kub(S - S0)**2 ! !Ktheta: kcal/mole/rad**2 !Theta0: degrees !Kub: kcal/mole/A**2 (Urey-Bradley) !S0: A ! !atom types KthetaTheta0 Kub S0 ! NR2c CP2c NR1c 130.00114.00 ! CP2c NR2c CP1c 130.00106.00 ! CP2c NR1c CP1c 130.00107.90 ! NR2c CP1c CP1c 130.00108.30 ! NR2c CP1c CE1c 45.80129.50 ! NR1c CP1c OcH42.00126.00 ! NR1c CP1c CP1c 130.00103.00 ! !Connection to the ser fragment !-- CT2 CT1 CP2c52.000 108. ! ALLOW ALI PEP POL ARO HB CT1 CP2c 50.000 109.5000 ! ALLOW PEP NH1 CT1 CP2c 50.000 107. ! ALLOW PEP POL ARO ALI NR2C CP2C CT1 40.00125.00 ! !Connection to the gly fragment !-- NR1C CT2 C 50.000 107. NR1c CT2 HB 48.000 108. CP2C NR1C CT2 36.00129.00 CP1C NR1C CT2 32.00123.40 ! DIHEDRALS ! !V(dihedral) = Kchi(1 + cos(n(chi) - delta)) ! !Kchi: kcal/mole !n: multiplicity !delta: degrees ! !atom types Kchin delta ! CP2C NR2C CP1C CP1C14. 2 180.00 ! CP2C NR1C CP1C CP1C14. 2 180.00 ! NR2C CP2C NR1C CP1C14. 2 180.00 ! NR2C CP1C CP1C NR1C 4. 2 180.00 ! NR1C CP2C NR2C CP1C 4. 2 180.00 ! CA1 CA2 CA3 CA4 3.1000 2 180.00 ! !barrier CA-CB CP1C CP1C CE1C HA1C 6.84 2 180.00 ! CP1C CP1C CE1C CA1 6.84 2 180.00 ! NR2C CP1C CE1C HA1C 6.84 2 180.00 ! NR2C CP1C CE1C CA1 6.84 2 180.00 ! ! !barrier CB-CG2 CP1C CE1C CA1 CA2 1.4 2 180.00 ! HA1C CE1C CA1 CA2 1.4 2 180.00 ! ! CP2C NR1C CP1C OCH 14.002 180.00 ! NR2C CP2C NR1C CT2 14.002 180.00 ! NR2C CP1C CP1C OCH 14.002 180.00 ! CP1C NR1C CP2C CT1 14.002 180.00 ! OCH CP1C NR1C CT2 14.002 180.00 ! CP1C NR2C CP2C CT1 14.002 180.00 ! CP1C CP1C NR1C CT2 14.002 180.00 ! CT1 CP2C NR1C CT2 14.002 180.00 ! ! ! Linking the chromophore and the glycine fragment OCCT2 NR1C 0. 1 0.00 ! NH1 CCT2 NR1c 0.6000 1 0.00 ! CP2C NR1C CT2 HB 0.032 3 0.00 ! CP2c NR1c CT2 C 0.032 3 0.00 ! CP1c NR1c CT2 HB 0.032 3 180.00 ! CP1c NR1c CT2 C 0.032 3 180.00 ! ! ! Linking the chromophore and the serine fragment CNH1 CT1 CP2C 0.2000 1 180.00 ! HNH1 CT1 CP2C 0. 1 0.00 ! NR2C CP2C CT1 HB 0.105 3 180.00 ! NR2C CP2C CT1 NH10.105 3 180.00 ! NR2C CP2C CT1 CT20.105 3 180.00 ! NR1C CP2C CT1 HB 0.105 3 0.00 ! IMPROPER ! !V(improper) = Kpsi(psi - psi0)**2 ! !Kpsi: kcal/mole/rad**2 !psi0: degrees !note that the second column of numbers (0) is ignored ! !atom types Kpsi psi0 ! CP2C NR2C NR1C CT1 0.5 0 0.00 CP2C NR1C NR2C CT1 0.5 0 0.00 ! CP1C NR1C CP1C OCH 0.5 0 0.00 CP1C CP1C NR1C OCH 0.5 0 0.00 ! NR1C CP1C CP2C CT2 0.45 0 0.00 NR1C CP2C CP1C CT2
Re: [gmx-users] Re: adding ff parameter of modified residue to charmm ff
bharat gupta wrote: The residue is a chromophore of Green Fluorescent Protein. The parameter file that I have got has the connection for serine and glycine :- For those of us who aren't fluent in CHARMM (or whatever this is), it would be more useful if you describe plainly the nature of the connection between your chromophore and the protein. If the bonds are simply between backbone atoms (which should be the case for the GFP chromophore, right?) then you specify the bonds within the .rtp file (making use of the +/- connection feature), otherwise you have to use specbond.dat to build the connections. -Justin !Connection to the ser fragment !-- CT2 CT1 CP2c52.000 108. ! ALLOW ALI PEP POL ARO HB CT1 CP2c 50.000 109.5000 ! ALLOW PEP NH1 CT1 CP2c 50.000 107. ! ALLOW PEP POL ARO ALI NR2C CP2C CT1 40.00125.00 ! NR1C CP2C CT1 35.00121.40 ! ! !Connection to the gly fragment !-- NR1C CT2 C 50.000 107. NR1c CT2 HB 48.000 108. CP2C NR1C CT2 36.00129.00 CP1C NR1C CT2 32.00123.40 On Thu, Mar 3, 2011 at 1:23 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 03/03/11, *bharat gupta * bharat.85.m...@gmail.com mailto:bharat.85.m...@gmail.com wrote: Hi, I followed the tutorial - http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field for updating the Charmm FF for my modified residue .. I added the residues to the .rtp file , then I added the new atom types in .atp file , The compound has some linkage with serine and glycine ... I want to know how and where shall I add the linkage parameters and the parameters (in bits) given below Without some idea what you mean by linkage with serine and glycine it's too hard to offer help. Mark (The parameter file of the compound looks like this ) .. BONDS ! !V(bond) = Kb(b - b0)**2 ! !Kb: kcal/mole/A**2 !b0: A ! !atom type Kb b0 CA1 CA2 305.00 1.3750 ! CA2 CA3 305.00 1.3750 ! CA3 CA4 305.00 1.3750 ! HPc CA1 340.000 1.08 ! HPc CA2 340.000 1.08 ! HPc CA3 340.000 1.08 ! HPc CA4 340.000 1.08 ! ANGLES ! !V(angle) = Ktheta(Theta - Theta0)**2 ! !V(Urey-Bradley) = Kub(S - S0)**2 ! !Ktheta: kcal/mole/rad**2 !Theta0: degrees !Kub: kcal/mole/A**2 (Urey-Bradley) !S0: A ! !atom types KthetaTheta0 Kub S0 ! NR2c CP2c NR1c 130.00114.00 ! CP2c NR2c CP1c 130.00106.00 ! CP2c NR1c CP1c 130.00107.90 ! NR2c CP1c CP1c 130.00108.30 ! NR2c CP1c CE1c 45.80129.50 ! NR1c CP1c OcH42.00126.00 ! NR1c CP1c CP1c 130.00103.00 ! !Connection to the ser fragment !-- CT2 CT1 CP2c52.000 108. ! ALLOW ALI PEP POL ARO HB CT1 CP2c 50.000 109.5000 ! ALLOW PEP NH1 CT1 CP2c 50.000 107. ! ALLOW PEP POL ARO ALI NR2C CP2C CT1 40.00125.00 ! !Connection to the gly fragment !-- NR1C CT2 C 50.000 107. NR1c CT2 HB 48.000 108. CP2C NR1C CT2 36.00129.00 CP1C NR1C CT2 32.00123.40 ! DIHEDRALS ! !V(dihedral) = Kchi(1 + cos(n(chi) - delta)) ! !Kchi: kcal/mole !n: multiplicity !delta: degrees ! !atom types Kchin delta ! CP2C NR2C CP1C CP1C14. 2 180.00 ! CP2C NR1C CP1C CP1C14. 2 180.00 ! NR2C CP2C NR1C CP1C14. 2 180.00 ! NR2C CP1C CP1C NR1C 4. 2 180.00 ! NR1C CP2C NR2C CP1C 4. 2 180.00 ! CA1 CA2 CA3 CA4 3.1000 2 180.00 ! !barrier CA-CB CP1C CP1C CE1C HA1C 6.84 2 180.00 ! CP1C CP1C CE1C CA1 6.84 2 180.00 ! NR2C CP1C CE1C HA1C 6.84 2 180.00 ! NR2C CP1C CE1C CA1 6.84 2 180.00 ! ! !barrier CB-CG2 CP1C CE1C CA1 CA2 1.4 2 180.00 ! HA1C CE1C CA1 CA2 1.4 2 180.00 ! ! CP2C NR1C CP1C OCH 14.002 180.00 ! NR2C CP2C NR1C CT2 14.002 180.00 ! NR2C CP1C CP1C OCH 14.002 180.00 ! CP1C NR1C CP2C CT1 14.002 180.00 ! OCH CP1C NR1C CT2 14.002 180.00 ! CP1C NR2C CP2C CT1 14.002 180.00 ! CP1C CP1C NR1C CT2 14.002 180.00 ! CT1 CP2C NR1C CT2 14.002 180.00 ! ! ! Linking the chromophore and the glycine fragment OCCT2 NR1C 0. 1 0.00 ! NH1 CCT2 NR1c 0.6000 1 0.00 ! CP2C NR1C CT2 HB 0.032 3 0.00 ! CP2c NR1c CT2 C 0.032 3 0.00 ! CP1c NR1c CT2 HB
Re: [gmx-users] Re: adding ff parameter of modified residue to charmm ff
Hi, 3 mar 2011 kl. 10.17 skrev gmx-users-requ...@gromacs.org: but I have the torsion angles , bond angles for my residue .. The problem is I don't know which one to put where as the charmm FF parameter that I have got doesnot match with the charmm ff parameter in gromacs.. that's y I am confused .. I don't fully understand but the parameters you listed are from CHARMM so to convert them to GROMACS you have to compare the functional forms (they are listed in the header for each type) with the GROMACS ones and also convert the units. Hi, I followed the tutorial - http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field for updating the Charmm FF for my modified residue .. I added the residues to the .rtp file , then I added the new atom types in .atp file , The compound has some linkage with serine and glycine ... I want to know how and where shall I add the linkage parameters and the parameters (in bits) given below (The parameter file of the compound looks like this ) .. BONDS ! !V(bond) = Kb(b - b0)**2 ! !Kb: kcal/mole/A**2 !b0: A ! !atom type Kb b0 CA1 CA2 305.00 1.3750 ! CA2 CA3 305.00 1.3750 ! CA3 CA4 305.00 1.3750 ! HPc CA1 340.000 1.08 ! HPc CA2 340.000 1.08 ! HPc CA3 340.000 1.08 ! HPc CA4 340.000 1.08 ! ANGLES ! !V(angle) = Ktheta(Theta - Theta0)**2 ! !V(Urey-Bradley) = Kub(S - S0)**2 ! !Ktheta: kcal/mole/rad**2 !Theta0: degrees !Kub: kcal/mole/A**2 (Urey-Bradley) !S0: A ! !atom types KthetaTheta0 Kub S0 ! NR2c CP2c NR1c 130.00114.00 ! CP2c NR2c CP1c 130.00106.00 ! CP2c NR1c CP1c 130.00107.90 ! NR2c CP1c CP1c 130.00108.30 ! NR2c CP1c CE1c 45.80129.50 ! NR1c CP1c OcH42.00126.00 ! NR1c CP1c CP1c 130.00103.00 ! !Connection to the ser fragment !-- CT2 CT1 CP2c52.000 108. ! ALLOW ALI PEP POL ARO HB CT1 CP2c 50.000 109.5000 ! ALLOW PEP NH1 CT1 CP2c 50.000 107. ! ALLOW PEP POL ARO ALI NR2C CP2C CT1 40.00125.00 ! !Connection to the gly fragment !-- NR1C CT2 C 50.000 107. NR1c CT2 HB 48.000 108. CP2C NR1C CT2 36.00129.00 CP1C NR1C CT2 32.00123.40 ! DIHEDRALS ! !V(dihedral) = Kchi(1 + cos(n(chi) - delta)) ! !Kchi: kcal/mole !n: multiplicity !delta: degrees ! !atom types Kchin delta ! CP2C NR2C CP1C CP1C14. 2 180.00 ! CP2C NR1C CP1C CP1C14. 2 180.00 ! NR2C CP2C NR1C CP1C14. 2 180.00 ! NR2C CP1C CP1C NR1C 4. 2 180.00 ! NR1C CP2C NR2C CP1C 4. 2 180.00 ! CA1 CA2 CA3 CA4 3.1000 2 180.00 ! !barrier CA-CB CP1C CP1C CE1C HA1C 6.84 2 180.00 ! CP1C CP1C CE1C CA1 6.84 2 180.00 ! NR2C CP1C CE1C HA1C 6.84 2 180.00 ! NR2C CP1C CE1C CA1 6.84 2 180.00 ! ! !barrier CB-CG2 CP1C CE1C CA1 CA2 1.4 2 180.00 ! HA1C CE1C CA1 CA2 1.4 2 180.00 ! ! CP2C NR1C CP1C OCH 14.002 180.00 ! NR2C CP2C NR1C CT2 14.002 180.00 ! NR2C CP1C CP1C OCH 14.002 180.00 ! CP1C NR1C CP2C CT1 14.002 180.00 ! OCH CP1C NR1C CT2 14.002 180.00 ! CP1C NR2C CP2C CT1 14.002 180.00 ! CP1C CP1C NR1C CT2 14.002 180.00 ! CT1 CP2C NR1C CT2 14.002 180.00 ! ! ! Linking the chromophore and the glycine fragment OCCT2 NR1C 0. 1 0.00 ! NH1 CCT2 NR1c 0.6000 1 0.00 ! CP2C NR1C CT2 HB 0.032 3 0.00 ! CP2c NR1c CT2 C 0.032 3 0.00 ! CP1c NR1c CT2 HB 0.032 3 180.00 ! CP1c NR1c CT2 C 0.032 3 180.00 ! ! ! Linking the chromophore and the serine fragment CNH1 CT1 CP2C 0.2000 1 180.00 ! HNH1 CT1 CP2C 0. 1 0.00 ! NR2C CP2C CT1 HB 0.105 3 180.00 ! NR2C CP2C CT1 NH10.105 3 180.00 ! NR2C CP2C CT1 CT20.105 3 180.00 ! NR1C CP2C CT1 HB 0.105 3 0.00 ! IMPROPER ! !V(improper) = Kpsi(psi - psi0)**2 ! !Kpsi: kcal/mole/rad**2 !psi0: degrees !note that the second column of numbers (0) is ignored ! !atom types Kpsi psi0 ! CP2C NR2C NR1C CT1 0.5 0 0.00 CP2C NR1C NR2C CT1 0.5 0 0.00 ! CP1C NR1C CP1C OCH 0.5 0 0.00 CP1C CP1C NR1C OCH 0.5 0 0.00 ! NR1C CP1C CP2C CT2 0.45 0 0.00 NR1C CP2C CP1C CT2 0.45 0 0.00 ! CP1C NR2C CP1C CE1C 220.0 0 0.00 CP1C CP1C NR2C CE1C 220.0 0 0.00 ! !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] ! !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j ! !atom
Re: [gmx-users] Re: adding ff parameter of modified residue to charmm ff
On 3/03/2011 11:42 PM, Justin A. Lemkul wrote: bharat gupta wrote: The residue is a chromophore of Green Fluorescent Protein. The parameter file that I have got has the connection for serine and glycine :- For those of us who aren't fluent in CHARMM (or whatever this is), it would be more useful if you describe plainly the nature of the connection between your chromophore and the protein. If the bonds are simply between backbone atoms (which should be the case for the GFP chromophore, right?) then you specify the bonds within the .rtp file (making use of the +/- connection feature), otherwise you have to use specbond.dat to build the connections. Agreed. However if things look anything like http://ca.wikipedia.org/wiki/Fitxer:The_chromophore_of_GFP.png then I'd make a single new residue for the whole chromophore and forget about specbond.dat. If you have to introduce new atom or interaction types, then you do that by analogy with the existing types, in consultation with chapter 5 of the manual and its CHARMM-equivalent. Mark !Connection to the ser fragment !-- CT2 CT1 CP2c52.000 108. ! ALLOW ALI PEP POL ARO HB CT1 CP2c 50.000 109.5000 ! ALLOW PEP NH1 CT1 CP2c 50.000 107. ! ALLOW PEP POL ARO ALI NR2C CP2C CT1 40.00125.00 ! NR1C CP2C CT1 35.00121.40 ! ! !Connection to the gly fragment !-- NR1C CT2 C 50.000 107. NR1c CT2 HB 48.000 108. CP2C NR1C CT2 36.00129.00 CP1C NR1C CT2 32.00123.40 On Thu, Mar 3, 2011 at 1:23 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 03/03/11, *bharat gupta * bharat.85.m...@gmail.com mailto:bharat.85.m...@gmail.com wrote: Hi, I followed the tutorial - http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field for updating the Charmm FF for my modified residue .. I added the residues to the .rtp file , then I added the new atom types in .atp file , The compound has some linkage with serine and glycine ... I want to know how and where shall I add the linkage parameters and the parameters (in bits) given below Without some idea what you mean by linkage with serine and glycine it's too hard to offer help. Mark (The parameter file of the compound looks like this ) .. BONDS ! !V(bond) = Kb(b - b0)**2 ! !Kb: kcal/mole/A**2 !b0: A ! !atom type Kb b0 CA1 CA2 305.00 1.3750 ! CA2 CA3 305.00 1.3750 ! CA3 CA4 305.00 1.3750 ! HPc CA1 340.000 1.08 ! HPc CA2 340.000 1.08 ! HPc CA3 340.000 1.08 ! HPc CA4 340.000 1.08 ! ANGLES ! !V(angle) = Ktheta(Theta - Theta0)**2 ! !V(Urey-Bradley) = Kub(S - S0)**2 ! !Ktheta: kcal/mole/rad**2 !Theta0: degrees !Kub: kcal/mole/A**2 (Urey-Bradley) !S0: A ! !atom types KthetaTheta0 Kub S0 ! NR2c CP2c NR1c 130.00114.00 ! CP2c NR2c CP1c 130.00106.00 ! CP2c NR1c CP1c 130.00107.90 ! NR2c CP1c CP1c 130.00108.30 ! NR2c CP1c CE1c 45.80 129.50 ! NR1c CP1c OcH42.00126.00 ! NR1c CP1c CP1c 130.00103.00 ! !Connection to the ser fragment !-- CT2 CT1 CP2c52.000 108. ! ALLOW ALI PEP POL ARO HB CT1 CP2c 50.000 109.5000 ! ALLOW PEP NH1 CT1 CP2c 50.000 107. ! ALLOW PEP POL ARO ALI NR2C CP2C CT1 40.00125.00 ! !Connection to the gly fragment !-- NR1C CT2 C 50.000 107. NR1c CT2 HB 48.000 108. CP2C NR1C CT2 36.00129.00 CP1C NR1C CT2 32.00123.40 ! DIHEDRALS ! !V(dihedral) = Kchi(1 + cos(n(chi) - delta)) ! !Kchi: kcal/mole !n: multiplicity !delta: degrees ! !atom types Kchin delta ! CP2C NR2C CP1C CP1C14. 2 180.00 ! CP2C NR1C CP1C CP1C14. 2 180.00 ! NR2C CP2C NR1C CP1C14. 2 180.00 ! NR2C CP1C CP1C NR1C 4. 2 180.00 ! NR1C CP2C NR2C CP1C 4. 2 180.00 ! CA1 CA2 CA3 CA4 3.1000 2 180.00 ! !barrier CA-CB CP1C CP1C CE1C HA1C 6.84 2 180.00 ! CP1C CP1C CE1C CA1 6.84 2 180.00 ! NR2C CP1C CE1C HA1C 6.84 2 180.00 ! NR2C CP1C CE1C CA1 6.84 2 180.00 ! ! !barrier CB-CG2 CP1C CE1C CA1 CA2 1.4 2 180.00 ! HA1C CE1C CA1 CA2 1.4 2 180.00 ! ! CP2C NR1C CP1C OCH 14.002 180.00 ! NR2C CP2C NR1C CT2 14.002 180.00 ! NR2C CP1C CP1C OCH 14.002 180.00 ! CP1C NR1C CP2C CT1 14.002 180.00 ! OCH CP1C NR1C CT2 14.002 180.00 ! CP1C NR2C CP2C CT1
[gmx-users] Re: adding ff parameter of modified residue to charmm ff
Hi, I followed the tutorial - http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field for updating the Charmm FF for my modified residue .. I added the residues to the .rtp file , then I added the new atom types in .atp file , The compound has some linkage with serine and glycine ... I want to know how and where shall I add the linkage parameters and the parameters (in bits) given below (The parameter file of the compound looks like this ) .. BONDS ! !V(bond) = Kb(b - b0)**2 ! !Kb: kcal/mole/A**2 !b0: A ! !atom type Kb b0 CA1 CA2 305.00 1.3750 ! CA2 CA3 305.00 1.3750 ! CA3 CA4 305.00 1.3750 ! HPc CA1 340.000 1.08 ! HPc CA2 340.000 1.08 ! HPc CA3 340.000 1.08 ! HPc CA4 340.000 1.08 ! ANGLES ! !V(angle) = Ktheta(Theta - Theta0)**2 ! !V(Urey-Bradley) = Kub(S - S0)**2 ! !Ktheta: kcal/mole/rad**2 !Theta0: degrees !Kub: kcal/mole/A**2 (Urey-Bradley) !S0: A ! !atom types KthetaTheta0 Kub S0 ! NR2c CP2c NR1c 130.00114.00 ! CP2c NR2c CP1c 130.00106.00 ! CP2c NR1c CP1c 130.00107.90 ! NR2c CP1c CP1c 130.00108.30 ! NR2c CP1c CE1c 45.80129.50 ! NR1c CP1c OcH42.00126.00 ! NR1c CP1c CP1c 130.00103.00 ! !Connection to the ser fragment !-- CT2 CT1 CP2c52.000 108. ! ALLOW ALI PEP POL ARO HB CT1 CP2c 50.000 109.5000 ! ALLOW PEP NH1 CT1 CP2c 50.000 107. ! ALLOW PEP POL ARO ALI NR2C CP2C CT1 40.00125.00 ! !Connection to the gly fragment !-- NR1C CT2 C 50.000 107. NR1c CT2 HB 48.000 108. CP2C NR1C CT2 36.00129.00 CP1C NR1C CT2 32.00123.40 ! DIHEDRALS ! !V(dihedral) = Kchi(1 + cos(n(chi) - delta)) ! !Kchi: kcal/mole !n: multiplicity !delta: degrees ! !atom types Kchin delta ! CP2C NR2C CP1C CP1C14. 2 180.00 ! CP2C NR1C CP1C CP1C14. 2 180.00 ! NR2C CP2C NR1C CP1C14. 2 180.00 ! NR2C CP1C CP1C NR1C 4. 2 180.00 ! NR1C CP2C NR2C CP1C 4. 2 180.00 ! CA1 CA2 CA3 CA4 3.1000 2 180.00 ! !barrier CA-CB CP1C CP1C CE1C HA1C 6.84 2 180.00 ! CP1C CP1C CE1C CA1 6.84 2 180.00 ! NR2C CP1C CE1C HA1C 6.84 2 180.00 ! NR2C CP1C CE1C CA1 6.84 2 180.00 ! ! !barrier CB-CG2 CP1C CE1C CA1 CA2 1.4 2 180.00 ! HA1C CE1C CA1 CA2 1.4 2 180.00 ! ! CP2C NR1C CP1C OCH 14.002 180.00 ! NR2C CP2C NR1C CT2 14.002 180.00 ! NR2C CP1C CP1C OCH 14.002 180.00 ! CP1C NR1C CP2C CT1 14.002 180.00 ! OCH CP1C NR1C CT2 14.002 180.00 ! CP1C NR2C CP2C CT1 14.002 180.00 ! CP1C CP1C NR1C CT2 14.002 180.00 ! CT1 CP2C NR1C CT2 14.002 180.00 ! ! ! Linking the chromophore and the glycine fragment OCCT2 NR1C 0. 1 0.00 ! NH1 CCT2 NR1c 0.6000 1 0.00 ! CP2C NR1C CT2 HB 0.032 3 0.00 ! CP2c NR1c CT2 C 0.032 3 0.00 ! CP1c NR1c CT2 HB 0.032 3 180.00 ! CP1c NR1c CT2 C 0.032 3 180.00 ! ! ! Linking the chromophore and the serine fragment CNH1 CT1 CP2C 0.2000 1 180.00 ! HNH1 CT1 CP2C 0. 1 0.00 ! NR2C CP2C CT1 HB 0.105 3 180.00 ! NR2C CP2C CT1 NH10.105 3 180.00 ! NR2C CP2C CT1 CT20.105 3 180.00 ! NR1C CP2C CT1 HB 0.105 3 0.00 ! IMPROPER ! !V(improper) = Kpsi(psi - psi0)**2 ! !Kpsi: kcal/mole/rad**2 !psi0: degrees !note that the second column of numbers (0) is ignored ! !atom types Kpsi psi0 ! CP2C NR2C NR1C CT1 0.5 0 0.00 CP2C NR1C NR2C CT1 0.5 0 0.00 ! CP1C NR1C CP1C OCH 0.5 0 0.00 CP1C CP1C NR1C OCH 0.5 0 0.00 ! NR1C CP1C CP2C CT2 0.45 0 0.00 NR1C CP2C CP1C CT2 0.45 0 0.00 ! CP1C NR2C CP1C CE1C 220.0 0 0.00 CP1C CP1C NR2C CE1C 220.0 0 0.00 ! !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] ! !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j ! !atom ignoredepsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 ! !CAc5.00 -0.07 1.992400 ! ALLOW ARO !! benzene (JES) CA15.00 -0.07 1.992400 ! ALLOW ARO CA25.00 -0.07 1.992400 ! ALLOW ARO CA35.00 -0.07 1.992400 ! ALLOW ARO CA45.00 -0.07 1.992400 ! ALLOW ARO CE1c 0.00 -0.068000 2.09 ! ! for propene, yin/adm jr., 12/95 CP1c 0.00 -0.05 1.80 ! ALLOW ARO ! adm jr., 10/23/91, imidazole solvation and sublimation CP2c 0.00 -0.05 1.80 ! ALLOW ARO ! adm jr., 10/23/91, imidazole solvation and sublimation CT3c
