[gmx-users] Re: adding ff parameter of modified residue to charmm ff
Jianguo Li
ljggmx at yahoo.com.sg
Thu Mar 3 09:58:57 CET 2011
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.monu at gmail.com>
To: Discussion list for GROMACS users <gmx-users at 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 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 : monu46010 at yahoo.com
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