On Fri, Mar 4, 2011 at 9:13 AM, Mark Abraham <[email protected]>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 >>> <[email protected]<mailto: >>> [email protected]>> wrote: >>> >>> >>> >>> On 03/03/11, *bharat gupta * <[email protected] >>> >>> <mailto:[email protected]>> 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 : [email protected] <mailto:[email protected]> >>>> >>>> >>> -- >>> gmx-users mailing list [email protected] >>> <mailto:[email protected]> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to [email protected] >>> <mailto:[email protected]>. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> >>> >>> >>> -- >>> 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 : [email protected] <mailto:[email protected]> >>> >>> >> > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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