[gmx-users] Atom type CB ERROR
Kashif
kashifzamir180.mk at gmail.com
Wed May 31 07:18:36 CEST 2017
I got parameter file (ligand.par) from swissparam. What should I add from
this file and where? means the topol.top file created during the
simulation, should I use that file to include CB parameter? Please find the
parameter data generated from swiss para and help me what to add regarding
CB atom type.
* ----
* Built parameters for ligand.mol2
* by user vzoete Mon May 29 09:38:13 CEST 2017
* ----
*
BONDS
HCMM CB 381.853 1.0840
HCMM CR 342.991 1.0930
HCMM C=O 334.643 1.1010
HCMM C=C 372.066 1.0830
CR CR 306.432 1.5080
CR NC=O 335.651 1.4360
CR NC=C 354.218 1.4460
NC=O C=O 419.491 1.3690
CR CB 356.737 1.4860
CB CB 401.068 1.3740
C=O CB 322.985 1.4570
C=O O=C 931.963 1.2220
NC=C C5B 478.144 1.3510
C=C NPYL 443.600 1.3680
C=C CB 360.335 1.4490
C=C C=C 684.039 1.3330
NPYL N5A 396.750 1.3390
NPYL C5A 453.459 1.3640
N5A C5B 594.297 1.3350
C5B N5B 320.682 1.3690
CSP CB 391.856 1.4240
CSP NSP 1193.344 1.1600
C5A N5B 599.191 1.3130
C5A N=C 491.098 1.3450
C=O N=C 725.204 1.2900
C=O C=C 328.526 1.4680
ANGLES
CB CB CB 48.145 119.9770
CB CB HCMM 40.517 120.5710
CB CB CR 57.788 120.4190
CB CB C=O 57.429 114.4750
NPYL C=C CB 71.966 120.0000
NPYL C=C C=C 70.239 122.3600
CB C=C C=C 43.035 117.5080
C=C NPYL N5A 64.769 133.2200
C=C NPYL C5A 61.747 130.2750
N5A NPYL C5A 92.404 112.0870
NPYL N5A C5B 125.076 101.5500
N5A C5B N5B 75.924 115.3690
N5A C5B NC=C 68.943 129.1250
N5B C5B NC=C 71.966 120.0000
C=C CB CB 51.240 119.6950
NPYL C5A N5B 72.829 110.8650
NPYL C5A N=C 76.859 121.7410
N5B C5A N=C 65.633 133.0200
C5B N5B C5A 86.791 103.7790
N=C C=O C=C 59.803 122.2530
N=C C=O HCMM 44.835 119.4910
C=C C=O HCMM 64.841 115.3500
C5A N=C C=O 89.741 109.9890
CB CB CSP 65.201 119.6140
C=C C=C C=O 39.221 111.2970
C=C C=C HCMM 38.502 121.0040
C=O C=C HCMM 35.047 117.2910
HCMM CR HCMM 37.134 108.8360
HCMM CR CR 45.770 110.5490
HCMM CR NC=O 53.255 107.6460
CR CR NC=O 75.564 109.9600
HCMM CR NC=C 51.743 109.8700
CR CR NC=C 81.321 108.6780
CR NC=O C=O 59.084 119.6000
CR NC=O CR 80.386 117.9090
CB CR HCMM 45.122 109.4910
CB CR CR 54.406 108.6170
CR CR CR 61.243 109.6080
CB C=O NC=O 79.234 112.4950
CB C=O O=C 52.823 119.9680
NC=O C=O O=C 65.273 127.1520
C5B NC=C CR 76.571 115.4830
CR NC=C CR 76.571 113.7030
CB CSP NSP 33.968 180.0000
DIHEDRALS
CB CB CB CB 3.500 2 180.00
CB CB CB HCMM 3.500 2 180.00
CB CB C=O NC=O 1.250 2 180.00
CB CB C=O O=C 1.250 2 180.00
CB CB CSP NSP 0.000 1 0.00
CB CB CR HCMM -0.210 2 180.00
CB CB CR HCMM 0.196 3 0.00
CB CB CR CR 0.225 2 180.00
CB CB CB C=C 3.500 2 180.00
CB CR CR HCMM 0.195 3 0.00
CB CR CR CR 0.150 3 0.00
CB CB CB CSP 3.500 2 180.00
CB C=O NC=O CR 3.000 2 180.00
C=C NPYL N5A C5B 0.000 1 0.00
C=C NPYL C5A N5B 3.000 2 180.00
C=C NPYL C5A N=C 3.000 2 180.00
C=C CB CB HCMM 1.000 2 180.00
C=C C=C C=O N=C 1.250 2 180.00
C=C C=C C=O HCMM 1.250 2 180.00
NPYL C=C CB CB 1.000 2 180.00
NPYL C=C C=C C=O 0.900 2 180.00
NPYL C=C C=C HCMM 0.900 2 180.00
NPYL N5A C5B N5B 3.500 2 180.00
NPYL N5A C5B NC=C 3.500 2 180.00
NPYL C5A N5B C5B 3.500 2 180.00
NPYL C5A N=C C=O 0.900 2 180.00
N5A NPYL C=C CB 3.000 2 180.00
N5A NPYL C=C C=C 3.000 2 180.00
N5A NPYL C5A N5B 2.000 2 180.00
N5A NPYL C5A N=C 2.000 2 180.00
N5A C5B N5B C5A 3.500 2 180.00
N5A C5B NC=C CR 1.800 2 180.00
C5B N5A NPYL C5A 2.000 2 180.00
C5B N5B C5A N=C 3.500 2 180.00
C5B NC=C CR HCMM 0.125 3 0.00
C5B NC=C CR CR 0.125 3 0.00
CB CB CB CR 3.500 2 180.00
CB CB C=C C=C 1.000 2 180.00
CB C=C NPYL C5A 3.000 2 180.00
CB C=C C=C C=O 0.900 2 180.00
CB C=C C=C HCMM 0.900 2 180.00
C5A NPYL C=C C=C 3.000 2 180.00
C5A N5B C5B NC=C 3.500 2 180.00
C5A N=C C=O C=C 0.900 2 180.00
C5A N=C C=O HCMM 0.900 2 180.00
N5B C5B NC=C CR 1.800 2 180.00
N5B C5A N=C C=O 0.900 2 180.00
CB CB CB C=O 3.500 2 180.00
N=C C=O C=C HCMM -0.145 1 0.00
N=C C=O C=C HCMM 0.760 2 180.00
N=C C=O C=C HCMM -0.235 3 0.00
HCMM CB CB HCMM 3.500 2 180.00
HCMM CB CB CSP 3.500 2 180.00
HCMM CB CB C=O 3.500 2 180.00
HCMM CR NC=O CR 0.390 3 0.00
HCMM CR NC=O C=O -1.050 1 0.00
HCMM CR NC=O C=O 0.681 2 180.00
HCMM CR NC=O C=O 0.011 3 0.00
HCMM CR CR HCMM 0.142 1 0.00
HCMM CR CR HCMM -0.693 2 180.00
HCMM CR CR HCMM 0.157 3 0.00
HCMM CR CR NC=C 0.150 3 0.00
HCMM CR NC=C CR 0.125 3 0.00
HCMM CR CR NC=O 0.213 3 0.00
HCMM C=O C=C HCMM -0.104 1 0.00
HCMM C=O C=C HCMM 0.811 2 180.00
HCMM C=O C=C HCMM 0.112 3 0.00
HCMM CB CB CR 3.500 2 180.00
HCMM CR CR CR 0.320 1 0.00
HCMM CR CR CR -0.315 2 180.00
HCMM CR CR CR 0.132 3 0.00
CR CR NC=C CR 0.125 3 0.00
CR NC=O C=O O=C -0.160 1 0.00
CR NC=O C=O O=C 3.147 2 180.00
CR NC=O C=O O=C -0.073 3 0.00
CR NC=O CR CR 0.150 3 0.00
CR CR NC=O C=O -0.513 1 0.00
CR CR NC=O C=O 0.347 2 180.00
CR CR NC=O C=O 0.474 3 0.00
NC=O CR CR NC=C 0.150 3 0.00
CR CR CR CR 0.051 1 0.00
CR CR CR CR 0.341 2 180.00
CR CR CR CR 0.166 3 0.00
IMPROPER
CB CB CB HCMM 1.079 0 0.00
CB C=O CB CB 1.943 0 0.00
C=O NC=O CB O=C 9.356 0 0.00
NC=O CR C=O CR -1.439 0 0.00
CR CR NC=O HCMM 0.000 0 0.00
CR HCMM NC=O HCMM 0.000 0 0.00
CR NC=C CR HCMM 0.000 0 0.00
CR HCMM CR HCMM 0.000 0 0.00
NC=C C5B CR CR -0.360 0 0.00
C5B N5A NC=C N5B 2.879 0 0.00
NPYL C=C N5A C5A 1.439 0 0.00
C=C CB NPYL C=C 1.439 0 0.00
CB CB C=C CB 2.231 0 0.00
CB CR CB CB 2.879 0 0.00
C=C C=O C=C HCMM 0.864 0 0.00
C5A N5B NPYL N=C 3.598 0 0.00
CR CR NC=C HCMM 0.000 0 0.00
CR HCMM NC=C HCMM 0.000 0 0.00
C=O N=C C=C HCMM 5.829 0 0.00
CR CR CB CR 0.000 0 0.00
CR CR CB HCMM 0.000 0 0.00
CR CR CR HCMM 0.000 0 0.00
CB CB CB CSP 2.519 0 0.00
NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
CB 0.000000 -0.070000 1.992400
C=C 0.000000 -0.068000 2.090000
NPYL 0.000000 -0.090000 1.720000
N5A 0.000000 -0.200000 1.850000
C5B 0.000000 -0.050000 2.040000
C5A 0.000000 -0.050000 2.040000
N5B 0.000000 -0.200000 1.850000
C=O 0.000000 -0.110000 2.000000
N=C 0.000000 -0.200000 1.850000
HCMM 0.000000 -0.022000 1.320000
CR 0.000000 -0.055000 2.175000 0.000000 -0.010000
1.900000
NC=O 0.000000 -0.200000 1.850000
NC=C 0.000000 -0.200000 1.850000
CSP 0.000000 -0.068000 2.080000
O=C 0.000000 -0.120000 1.700000 0.000000 -0.120000
1.400000
NSP 0.000000 -0.200000 1.850000
regards
kashif
On Mon, May 29, 2017 at 2:36 PM, Kashif <kashifzamir180.mk at gmail.com> wrote:
> dear sir
>
> I prepared ligand topology and coordinate file using swiss param tool.
> Then I simulate my protein with CHARMM FORCE FILED. After giving command
>
> grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
>
> i found this error....
>
> Fatal error:
> Atomtype CB not found
>
> Kindly help to resolve this error.
>
> regards
>
> kashif
>
>
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