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 <[email protected]> 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 <[email protected]> > *To:* Discussion list for GROMACS users <[email protected]> > *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 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 52.000 108.0000 ! ALLOW ALI PEP POL ARO > HB CT1 CP2c 50.000 109.5000 ! ALLOW PEP > NH1 CT1 CP2c 50.000 107.0000 ! ALLOW PEP POL ARO ALI > NR2C CP2C CT1 40.00 125.00 ! > > > > !Connection to the gly fragment > !------------------------------ > NR1C CT2 C 50.000 107.0000 > NR1c CT2 HB 48.000 108.0000 > 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 14.0000 2 180.00 ! > CP2C NR1C CP1C CP1C 14.0000 2 180.00 ! > NR2C CP2C NR1C CP1C 14.0000 2 180.00 ! > NR2C CP1C CP1C NR1C 4.0000 2 180.00 ! > NR1C CP2C NR2C CP1C 4.0000 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 0.0000 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 0.0000 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 5.000000 -0.070000 1.992400 ! ALLOW ARO > ! ! benzene (JES) > CA1 5.000000 -0.070000 1.992400 ! ALLOW ARO > CA2 5.000000 -0.070000 1.992400 ! ALLOW ARO > CA3 5.000000 -0.070000 1.992400 ! ALLOW ARO > CA4 5.000000 -0.070000 1.992400 ! ALLOW ARO > CE1c 0.000000 -0.068000 2.090000 ! > ! for propene, yin/adm jr., 12/95 > CP1c 0.000000 -0.050000 1.800000 ! ALLOW ARO > ! adm jr., 10/23/91, imidazole solvation and sublimation > CP2c 0.000000 -0.050000 1.800000 ! ALLOW ARO > ! adm jr., 10/23/91, imidazole solvation and sublimation > CT3c 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 > ! ALLOW ALI > ! methane/ethane a.i. and ethane pure solvent, adm jr, > 2/3/92 > ! > Hch -2.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC > ! same as TIP3P hydrogen, adm jr., 7/20/89 > HAc 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC > ! methane/ethane a.i. and ethane pure solvent, adm jr, > 2/3/92 > HA1c 0.000000 -0.031000 1.250000 ! > ! for propene, yin/adm jr., 12/95 > HPc 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 > ! ALLOW ARO > ! JES 8/25/89 values from Jorgensen fit to hydration energy > ! > NR1c 0.000000 -0.200000 1.850000 ! ALLOW ARO > ! His, adm jr., 9/4/89 > NR2c 0.000000 -0.200000 1.850000 ! ALLOW ARO > ! His, adm jr., 9/4/89 > ! > !Och 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 > ! ALLOW PEP POL > ! ! This 1,4 vdW allows the C5 dipeptide minimum to > exist.(LK) > Och 0.000000 -0.120000 1.700000! ALLOW PEP POL, suppression du > terme 1,4 (N.R. 10/2000) > OHc 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO > ! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P) > > HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use > ! READ PARAM APPEND CARD > ! to append hbond parameters from the file: par_hbond.inp > > END > > > -- > Bharat > Ph.D. Candidate > Room No. : 7202A, 2nd Floor > Biomolecular Engineering Laboratory > Division of Chemical Engineering and Polymer Science > Pusan National University > Busan -609735 > South Korea > Lab phone no. - +82-51-510-3680, +82-51-583-8343 > Mobile no. - 010-5818-3680 > E-mail : [email protected] > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : [email protected]
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