[gmx-users] Re: adding ff parameter of modified residue to charmm ff
Mark Abraham
Mark.Abraham at anu.edu.au
Fri Mar 4 08:13:29 CET 2011
On 3/03/2011 11:42 PM, Justin A. Lemkul wrote:
>
>
> 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.
Agreed. However if things look anything like
http://ca.wikipedia.org/wiki/Fitxer:The_chromophore_of_GFP.png then I'd
make a single new residue for the whole chromophore and forget about
specbond.dat. If you have to introduce new atom or interaction types,
then you do that by analogy with the existing types, in consultation
with 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.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>
>>
>
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