[gmx-users] Atom type CB ERROR
Justin Lemkul
jalemkul at vt.edu
Wed May 31 13:54:29 CEST 2017
On 5/31/17 1:18 AM, Kashif wrote:
> 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.
>
These are all new parameters, so you need all of them. Hopefully it also
supplied you with nonbonded parameters for all those types. I'm sure it did,
but I have no experience with SwissParam.
-Justin
> * ----
> * 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
>>
>>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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