[gmx-users] Re: adding ff parameter of modified residue to charmm ff
bharat gupta
bharat.85.monu at gmail.com
Thu Mar 3 04:31:38 CET 2011
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110302/899da809/attachment.html>
More information about the gromacs.org_gmx-users
mailing list