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jianchaoyv

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[交流] 【求助】怎么看力场文件？已有2人参与

!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
!
C    0.000000  -0.110000    2.000000 ! ALLOW PEP POL ARO
            ! NMA pure solvent, adm jr., 3/3/93
CA    0.000000  -0.070000    1.992400 ! ALLOW ARO
            ! benzene (JES)
CC    0.000000  -0.070000    2.000000 ! ALLOW PEP POL ARO
            ! adm jr. 3/3/92, acetic acid heat of solvation
CD    0.000000  -0.070000    2.000000 ! ALLOW  POL
            ! adm jr. 3/19/92, acetate a.i. and dH of solvation
CE1 0.000000  -0.068000    2.090000 !
! for propene, yin/adm jr., 12/95
CE2 0.000000  -0.064000    2.080000 !
! for ethene, yin/adm jr., 12/95
CM    0.000000  -0.110000    2.100000 ! ALLOW HEM
            ! Heme (6-liganded): CO ligand carbon (KK 05/13/91)
CP1 0.000000  -0.020000    2.275000 0.000000  -0.010000    1.900000 ! ALLOW ALI
            ! alkane update, adm jr., 3/2/92
CP2 0.000000  -0.055000    2.175000 0.000000  -0.010000    1.900000 ! ALLOW ALI
            ! alkane update, adm jr., 3/2/92
CP3 0.000000  -0.055000    2.175000 0.000000  -0.010000    1.900000 ! ALLOW ALI
            ! alkane update, adm jr., 3/2/92
CPA 0.000000  -0.090000    1.800000 ! ALLOW HEM
            ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPB 0.000000  -0.090000    1.800000 ! ALLOW HEM
            ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPH1 0.000000  -0.050000    1.800000 ! ALLOW ARO
            ! adm jr., 10/23/91, imidazole solvation and sublimation
CPH2 0.000000  -0.050000    1.800000 ! ALLOW ARO
            ! adm jr., 10/23/91, imidazole solvation and sublimation
CPM 0.000000  -0.090000    1.800000 ! ALLOW HEM
            ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPT 0.000000  -0.090000    1.800000 0.000000  -0.090000    1.900000 ! ALLOW ARO
            ! benzene (JES)
CS    0.000000  -0.110000    2.200000 ! ALLOW SUL
            ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92
CT1 0.000000  -0.020000    2.275000 0.000000  -0.010000    1.900000 ! ALLOW ALI
            ! isobutane pure solvent properties, adm jr, 2/3/92
CT2 0.000000  -0.055000    2.175000 0.000000  -0.010000    1.900000 ! ALLOW ALI
            ! propane pure solvent properties, adm jr, 2/3/92
CT3 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
CY    0.000000  -0.070000    1.992400 ! ALLOW ARO
            ! TRP, JWK 08/29/89
! carbon wildcards, following atom order is essential for accurate results
!C*    0.000000  -0.070000    2.000000
!CP% 0.000000  -0.090000    1.800000
!C%1 0.000000  -0.020000    2.275000 0.000000  -0.010000    1.900000
!C%2 0.000000  -0.055000    2.175000 0.000000  -0.010000    1.900000
!C%3 0.000000  -0.080000    2.060000 0.000000  -0.010000    1.900000
!CPH+ 0.000000  -0.050000    1.800000
!C    0.000000  -0.110000    2.000000
!CA    0.000000  -0.070000    1.992400
!CE1 0.000000  -0.068000    2.090000
!CE2 0.000000  -0.064000    2.080000
!CM    0.000000  -0.110000    2.100000
!CP3 0.000000  -0.055000    2.175000 0.000000  -0.010000    1.900000 ! ALLOW ALI
!CPT 0.000000  -0.090000    1.800000 0.000000  -0.090000    1.900000
!CS    0.000000  -0.110000    2.200000
!CY    0.000000  -0.070000    1.992400

H    0.000000  -0.046000    0.224500 ! ALLOW PEP POL SUL ARO ALC
            ! same as TIP3P hydrogen, adm jr., 7/20/89
HA    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
HE1 0.000000  -0.031000    1.250000 !
! for propene, yin/adm jr., 12/95
HE2 0.000000  -0.026000    1.260000 !
! for ethene, yin/adm jr., 12/95
HB    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
HC    0.000000  -0.046000    0.224500 ! ALLOW POL
            ! new, small polar Hydrogen, see also adm jr. JG 8/27/89
HP    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
HR1 0.000000  -0.046000    0.900000 ! ALLOW ARO
            ! adm jr., 6/27/90, his
HR2 0.000000  -0.046000    0.700000 ! ALLOW ARO
            ! adm jr., 6/27/90, his
HR3 0.000000  -0.007800    1.468000 ! ALLOW ARO
            ! adm jr., 3/24/92, maintain old aliphatic H VDW params
HS    0.000000  -0.100000    0.450000 ! ALLOW SUL
            ! methanethiol pure solvent, adm jr., 6/22/92
HT    0.000000  -0.046000    0.224500 ! ALLOW WAT
            !TIP3P HYDROGEN PARAMETERS, adm jr., NBFIX obsolete
! hydrogen wildcards
!H*    0.000000  -0.046000    0.224500
!HA    0.000000  -0.022000    1.320000
!HE1 0.000000  -0.031000    1.250000
!HE2 0.000000  -0.026000    1.260000
!HB    0.000000  -0.022000    1.320000
!HP    0.000000  -0.030000    1.358200 0.000000  -0.030000    1.358200
!HR1 0.000000  -0.046000    0.900000
!HR2 0.000000  -0.046000    0.700000
!HR3 0.000000  -0.007800    1.468000
!HS    0.000000  -0.100000    0.450000
!
N    0.000000  -0.200000    1.850000 0.000000  -0.000100    1.850000 ! ALLOW PRO
            ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NC2 0.000000  -0.200000    1.850000 ! ALLOW POL
            ! JG 8/27/89; note: NH1 in ARG was changed to NC2.
NH1 0.000000  -0.200000    1.850000 0.000000  -0.200000    1.550000 ! ALLOW PEP POL ARO
            ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK)
NH2 0.000000  -0.200000    1.850000 ! ALLOW POL
            ! adm jr.
NH3 0.000000  -0.200000    1.850000 ! ALLOW POL
            ! adm jr.
NP    0.000000  -0.200000    1.850000 ! ALLOW  PRO
            ! N-terminal proline; from 6-31g* +ProNH2  RLD 9/28/90
NPH 0.000000  -0.200000    1.850000 ! ALLOW HEM
            ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NR1 0.000000  -0.200000    1.850000 ! ALLOW ARO
            ! His, adm jr., 9/4/89
NR2 0.000000  -0.200000    1.850000 ! ALLOW ARO
            ! His, adm jr., 9/4/89
NR3 0.000000  -0.200000    1.850000 ! ALLOW ARO
            ! His, adm jr., 9/4/89
NY    0.000000  -0.200000    1.850000 ! ALLOW ARO
            ! trp, JWK
! nitrogen wildcards
!N*    0.000000  -0.200000    1.850000
!N    0.000000  -0.200000    1.850000 0.000000  -0.000100    1.850000
!NH1 0.000000  -0.200000    1.850000 0.000000  -0.200000    1.550000
!
O    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)
OB    0.000000  -0.120000    1.700000 0.000000  -0.120000    1.400000 ! ALLOW PEP POL ARO
            ! adm jr., 10/17/90, acetic acid carbonyl O
OC    0.000000  -0.120000    1.700000 ! ALLOW POL ION
            ! JG 8/27/89
OH1 0.000000  -0.152100    1.770000 ! ALLOW ALC ARO
            ! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P)
OM    0.000000  -0.120000    1.700000 ! ALLOW HEM
            ! Heme (6-liganded): CO ligand oxygen (KK 05/13/91)
OS    0.000000  -0.152100    1.770000 ! ALLOW ALC ARO
            ! adm jr. 9/17/90, avoid O* wildcard
OT    0.000000  -0.152100    1.768200 ! ALLOW WAT
            !TIP3P OXYGEN PARAMETERS, adm jr., NBFIX obsolete
! oxygen wildcards
!O*    0.000000  -0.120000    1.700000 0.000000  -0.120000    1.400000
!OC    0.000000  -0.120000    1.700000
!OH1 0.000000  -0.152100    1.770000
!OM    0.000000  -0.120000    1.700000
!OS    0.000000  -0.152100    1.770000
!OT    0.000000  -0.152100    1.768200

!CAL 0.000000  -0.120000    1.710000 ! ALLOW ION
!             !Calcium (BP)
FE    0.010000 0.000000    0.650000 ! ALLOW HEM
            ! Heme (6-liganded): Iron atom (KK 05/13/91)
S    0.000000  -0.450000    2.000000 ! ALLOW SUL ION
            ! adm jr., 3/3/92, methanethiol/ethylmethylsulfide pure solvent
SM    0.000000  -0.380000    1.975000 ! ALLOW  SUL  ION
            ! adm jr., 3/3/92, dimethyldisulphide pure solvent
SS    0.000000  -0.470000    2.200000 ! ALLOW  SUL
            ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92
ZN    0.000000  -0.250000    1.090000 ! ALLOW  ION
            ! RHS March 18, 1990
DUM 0.000000  -0.000000    0.000000 !
            ! dummy atom
HE    0.000000  -0.021270    1.4800 !
            ! helium, experimental pot. energy surface, adm jr., 12/95
NE    0.000000  -0.086000    1.5300
            ! neon, semiempirical pot. energy surface, adm jr., 12/95
!lipids section
HOL    0.0    -0.046    0.2245
HAL1    0.0    -0.022    1.3200 ! alkane, 3/92
HAL2    0.0    -0.028    1.3400 ! alkane, yin and mackerell, 4/98
HAL3    0.0    -0.024    1.3400 ! alkane, yin and mackerell, 4/98
HCL    0.0    -0.046    0.2245 ! ethanolamine
!HT    0.0    -0.046    0.2245
HL    0.0    -0.046    0.7 ! polar H on NC4+
HEL1    0.0    -0.031    1.25 ! alkene, yin,adm jr., 12/95
HEL2    0.0    -0.026    1.26 ! alkene, yin,adm jr., 12/95
!
CL    0.0    -0.070    2.00 ! methyl acetate update
CTL1    0.0    -0.0200 2.275 0.0 -0.01 1.9 ! alkane, 3/92
CTL2    0.0    -0.0560 2.010 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr.
CTL3    0.0    -0.0780 2.040 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr.
CTL5    0.0    -0.0800 2.06  0.0 -0.01 1.9 ! old CTL3
                                                ! maintained for tetramethylammonium
CEL1    0.0    -0.068    2.09 ! alkene, yin,adm jr., 12/95
CEL2    0.0    -0.064    2.08 ! alkene, yin,adm jr., 12/95
!
OBL    0.0    -0.12    1.70  0.0 -0.12 1.4
OCL    0.0    -0.12    1.70
O2L    0.0    -0.12    1.70
OHL    0.0    -0.1521 1.77
OSL    0.0    -0.1521 1.77
!OT    0.0    -0.1521 1.7682
!
NH3L    0.0    -0.20    1.85  ! ethanolamine
NTL    0.0    -0.20    1.85  ! as all other nitogens
!
SL    0.0    -0.47    2.1 ! methylsulfate
PL    0.0    -0.585    2.15  ! ADM Jr.
!DUM    0.0    -0.00    0.0 ! dummy atom
!
! ions, note lack of NBFIXes
!
SOD    0.0    -0.0469 1.36375 ! sodium
               ! D. Beglovd and B. Roux, dA=-100.8 kcal/mol
POT    0.0    -0.0870 1.76375 ! potassium
               ! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol
CLA    0.0    -0.150    2.27    ! chloride
               ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol
CAL    0.0    -0.120    1.367 ! Calcium
               ! S. Marchand and B. Roux, dA = -384.8 kcal/mol
MG    0.0    -0.0150 1.18500 ! Magnesium
               ! B. Roux dA = -441.65
CES    0.0    -0.1900 2.100
               ! Cesium, so far untested.
怎样看力场文件？比如：文献中碳碳的epsilon=0.086Kcal/mol,碳氧的epsilon=0.114333，在上面给的参数中碳碳的epsilon是多少？碳氧的epsilon是多少？

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1楼 2010-06-23 20:12:41

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ghcacj

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lei0736(金币+1):谢谢 2010-06-24 10:26:43

你这里似乎没有给出LJ参数，看起来好象是键伸缩的参数。

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2楼2010-06-23 20:26:59

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ghcacj(金币+5):谢谢 2010-06-24 10:05:15

这是charmm 力场的文件, top 和par 都有详细的注释, 以!开头
这里面有你想要的很多信息

!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
表示每对Eps 的数值为两个原子的几何平均

!atom  ignored epsilon    Rmin/2 ignored eps,1-4    Rmin/2,1-4
表示第三项是Eps 的数值

不清楚你说的C 和O 是什么类型,
举个羰基C,O的例子
CC    0.000000  -0.070000    2.000000 ! ALLOW PEP POL ARO
OC    0.000000  -0.120000    1.700000 ! ALLOW POL ION
上面两行是这两个原子的, 为什么这两行是? 这是常识, 入行必须知道
碳碳的epsilon=-sqrt(0.07*0.07), 碳氧的epsilon=-sqrt(0.07*0.12)
不同原子类型的参数天差地别, 不同力场的参数也是各自为政

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3楼2010-06-24 09:22:34

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