Re: [gmx-users] Re: adding ff parameter of modified residue to charmm ff

Mark Abraham Thu, 03 Mar 2011 23:14:03 -0800

On 3/03/2011 11:42 PM, Justin A. Lemkul wrote:

bharat gupta wrote:
The residue is a chromophore of Green Fluorescent Protein. Theparameter file that I have got has the connection for serine andglycine :-
For those of us who aren't fluent in CHARMM (or whatever this is), itwould be more useful if you describe plainly the nature of theconnection between your chromophore and the protein. If the bonds aresimply between backbone atoms (which should be the case for the GFPchromophore, right?) then you specify the bonds within the .rtp file(making use of the +/- connection feature), otherwise you have to usespecbond.dat to build the connections.

Agreed. However if things look anything likehttp://ca.wikipedia.org/wiki/Fitxer:The_chromophore_of_GFP.png then I'dmake a single new residue for the whole chromophore and forget aboutspecbond.dat. If you have to introduce new atom or interaction types,then you do that by analogy with the existing types, in consultationwith chapter 5 of the manual and its CHARMM-equivalent.


Mark

!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 ! NR1C CP2C CT1 35.00 121.40! !

!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

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_Fieldfor

    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 CP1c130.00 106.00 ! CP2c NR1c CP1c 130.00 107.90 !NR2c CP1c CP1c 130.00 108.30 ! NR2c CP1c CE1c 45.80129.50 ! 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 48.000108.0000

    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 CP1CCP1C 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 NR2CCP1C 4.0000 2 180.00 ! CA1 CA2 CA3 CA4 3.10002 180.00 !


    !barrier CA-CB

CP1C CP1C CE1C HA1C 6.84 2 180.00 ! CP1C CP1C CE1CCA1 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 CA1CA2 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 CCT2 NR1c 0.6000 1 0.00 ! CP2C NR1C CT2 HB0.032 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 CT1NH1 0.105 3 180.00 ! NR2C CP2C CT1 CT2 0.1053 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 NR1CCP2C 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,1-4Rmin/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 -0.0100001.900000 ! 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 -0.0300001.358200 ! 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), thenuse

                     ! 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 : monu46...@yahoo.com <mailto:monu46...@yahoo.com>


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--
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 : monu46...@yahoo.com <mailto:monu46...@yahoo.com>


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Re: [gmx-users] Re: adding ff parameter of modified residue to charmm ff

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