[gmx-users] Re: Adding chromophore parameters to the charmm force field
Justin A. Lemkul
jalemkul at vt.edu
Wed Feb 23 12:54:16 CET 2011
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
If you have specific implementation questions based on this information, post
those. Right now, your question is too broad for anyone to invest the
significant amount of time it would take to walk you through the whole process.
-Justin
bharat gupta wrote:
> 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 <mailto:monu46010 at yahoo.com>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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