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

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 3 13:42:19 CET 2011



bharat gupta wrote:
> The residue is a chromophore of Green Fluorescent Protein. The parameter 
> file that I have got has the connection for serine and glycine :-
> 

For those of us who aren't fluent in CHARMM (or whatever this is), it would be 
more useful if you describe plainly the nature of the connection between your 
chromophore and the protein.  If the bonds are simply between backbone atoms 
(which should be the case for the GFP chromophore, right?) then you specify the 
bonds within the .rtp file (making use of the +/- connection feature), otherwise 
you have to use specbond.dat to build the connections.

-Justin

> !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.abraham at anu.edu.au 
> <mailto:mark.abraham at anu.edu.au>> wrote:
> 
> 
> 
>     On 03/03/11, *bharat gupta * <bharat.85.monu at gmail.com
>     <mailto:bharat.85.monu at gmail.com>> wrote:
>>     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
> 
>     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 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 <mailto: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 <mailto:monu46010 at yahoo.com>
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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