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

bharat gupta bharat.85.monu at gmail.com
Thu Mar 3 10:16:28 CET 2011


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 <ljggmx at 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.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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-- 
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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