[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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