[gmx-users] Re: Adding chromophore parameters to the charmm force field
bharat gupta
bharat.85.monu at gmail.com
Wed Feb 23 07:40:13 CET 2011
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 : monu46010 at yahoo.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110222/671dfe4f/attachment.html>
More information about the gromacs.org_gmx-users
mailing list