[gmx-users] DENIZ-senin yapacagina benzer birsey yapmis, residue eklemis..
Emine Deniz Tekin
edeniztekin at gmail.com
Fri Mar 4 08:38:55 CET 2011
On Fri, Mar 4, 2011 at 9:13 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> 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_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 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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