Hi, I have obtained the chromophore parameters of the GFP for charmm force field but I am not able to find it out how to add it to the charmm FF file.. I have two files one is the topology file , which looks like this :-
* 22 1 MASS 13 CP2c 12.01100 C ! his CE1 carbon MASS 14 NR2c 14.00700 N ! neutral his unprotonated ring nitrogen MASS 15 NR1c 14.00700 N ! neutral his protonated ring nitrogen MASS 16 CP1c 12.01100 C ! his CG and CD2 carbons MASS 17 Och 15.99900 O ! carbonyl oxygen MASS 18 CE1c 12.01100 C ! for alkene; RHC=CR MASS 19 HA1c 1.00800 H ! for alkene; RHC=CR MASS 41 CA4 12.01100 C ! aromatic C MASS 42 HPc 1.00800 H ! aromatic H MASS 43 OHc 15.99900 O ! from OH1 MASS 44 Hch 1.00800 H ! polar H MASS 45 CT3c 12.01100 C ! aliphatic sp3 C for CH3 MASS 46 HAc 1.00800 H ! nonpolar H MASS 47 CA1 12.01100 C ! aromatic C MASS 48 CA2 12.01100 C ! aromatic C MASS 49 CA3 12.01100 C ! aromatic C DECL -CA DECL -C DECL -O DECL +N DECL +HN DECL +CA DEFA FIRS NTER LAST CTER AUTO ANGLES DIHE AUTOGENERATE ANGLES DIHE DEFA FIRS NONE LAST NONE RESI CRO 0.000 GROUP ! Imidazolinone ring ATOM C1 CP2c 0.76 ATOM N2 NR2c -0.55 ATOM N3 NR1c -0.64 ATOM C2 CP1c 0.80 ATOM O2 Och -0.61 ATOM CA CP1c 0.24 ! GROUP ! Charges from propene ATOM CB CE1c -0.10 ATOM HB HA1c 0.10 ! GROUP ! Tyr ring : charges from charmm22 ATOM CG2 CA1 0.00 ATOM CD1 CA2 -0.115 ATOM HD1 HPc 0.115 ATOM CD2 CA2 -0.115 ATOM HD2 HPc 0.115 ATOM CE1 CA3 -0.115 ATOM HE1 HPc 0.115 ATOM CE2 CA3 -0.115 ATOM HE2 HPc 0.115 ATOM CZ CA4 0.11 ATOM OH Ohc -0.54 ATOM HH Hch 0.43 ! !Glycine part / C=O taken from Charmm22 GROUP ATOM CAg CT2 -0.18 ! | ATOM HA1 HB 0.09 ! | ATOM HA2 HB 0.09 ! HA1-CA-HA2 GROUP ! | ATOM C C 0.51 ! | ATOM O O -0.51 ! C=O ! !Serine part / taken from Charmm22 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CAs CT1 0.07 ! | HB1 ATOM HA HB 0.09 ! | | GROUP ! HA-CA--CB--OG ATOM CBs CT2 0.05 ! | | \ ATOM HB1 HA 0.09 ! | HB2 HG1 ATOM HB2 HA 0.09 ! O=C ATOM OG1 OH1 -0.66 ! | ATOM HG1 H 0.43 Other file is the parameter file :- ! GFP Chromophore parameters, protonated form ! 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 ! Ohc Hch 545 0.96 ! Ohc CA4 334.3 1.4110 ! HA1c CE1c 360.500 1.10 ! NR1c CP1c 400.000 1.41 ! NR1c CP2c 400.000 1.39 ! NR2c CP2c 400.000 1.30 ! NR2c CP1c 400.000 1.40 ! CP1c CP1c 410.000 1.49 ! CP1c CE1c 560 1.36 ! CP1c Och 807 1.22 ! CE1c CA1 370 1.45 ! NR1c CT2 352 1.45 ! CP2c CT1 320 1.49 ! 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 ! OcH CP1c CP1c 38.00 132.00 ! CP1c CP1c CE1c 45.80 122.00 ! CP1c CE1c CA1 130.00 130.00 ! CP1c CE1c HA1c 42.00 114.00 ! CE1c CA1 CA2 45.80 121.00 HA1c CE1c CA1 42.00 116.00 ! CA1 CA2 CA3 40.000 120.00 35.00 2.41620 CA2 CA1 CA2 40.000 120.00 35.00 2.41620 CA2 CA3 CA4 40.000 120.00 35.00 2.41620 CA3 CA4 CA3 40.000 120.00 35.00 2.41620 ! HPc CA3 CA4 30.000 120.00 22.00 2.15250 HPc CA3 CA2 30.000 120.00 22.00 2.15250 HPc CA2 CA3 30.000 120.00 22.00 2.15250 HPc CA2 CA1 30.000 120.00 22.00 2.15250 ! Ohc CA4 CA3 45.200 120.0000 ! ALLOW ARO ALC HcH Ohc CA4 65.000 108.0000 ! ALLOW ALC ARO ! !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 ! 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 ! CA2 CA1 CA2 CA3 3.1000 2 180.00 ! CA2 CA3 CA4 CA3 3.1000 2 180.00 ! !OCh CAC CAC CAC 3.1000 2 180.00 ! CA2 CA3 CA4 OhC 3.1000 2 180.00 ! CA1 CA2 CA3 HPC 4.2000 2 180.00 ! CA2 CA1 CA2 HPC 4.2000 2 180.00 ! CA3 CA4 CA3 HPC 4.2000 2 180.00 ! HPC CA2 CA3 CA4 4.2000 2 180.00 ! HPC CA2 CA3 HPC 2.4000 2 180.00 ! !HCH OCh CAC CAC 0.9900 2 180.00 ! HCH OhC CA4 CA3 0.9900 2 180.00 ! HPC CA3 CA4 OhC 4.2000 2 180.00 ! ! CP2C NR2C CP1C CE1C 3.000 2 180.00 ! NR1C CP1C CP1C CE1C 3.00 2 180.00 ! OCH CP1C CP1C CE1C 2.00 2 180.00 ! CE1C CA1 CA2 HPC 4.20 2 180.00 ! CE1C CA1 CA2 CA3 3.10 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 ! NR1C CP2C CT1 NH1 0.105 3 0.00 ! NR1C CP2C CT1 CT2 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 ! CE1C CP1C CA1 HA1C 30.0 0 0.00 CE1C CA1 CP1C HA1C 30.0 0 0.00 Can anybody jus tell it how to do .. as I have posted this question earlier in the forum and got chapter 5 to read as suggestion ?? ... but I am a bit confused ...how to do it -- 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]
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