[gmx-users] Vacuum lig.itp
Martina Bertsch, PhD
mbe404 at lulu.it.northwestern.edu
Fri Feb 20 01:17:01 CET 2004
Thank you very much, Pedro. I was missing the "function" column in my
lig.itp. I enclosed the corrected itp for other users' reference.
[ moleculetype ]
;name nrexcl
DRG 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 CH3 1 DRG CAO 1 0.000 15.035
2 C 1 DRG CAM 1 0.380 12.011
3 O 1 DRG OAN 1 -0.380 15.9994
4 N 1 DRG NAL 2 -0.280 14.0067
5 H 1 DRG HAB 2 0.280 1.008
6 CH2 1 DRG CAK 3 0.000 14.027
etc.
[ bonds ]
; ai aj fn gromos type
1 2 2 gb_26
2 3 2 gb_4
2 4 2 gb_9
etc.
[ angles ]
; ai aj ak fn gromos type
1 2 3 2 ga_29
1 2 4 2 ga_18
3 2 4 2 ga_32
2 4 5 2 ga_31
2 4 6 2 ga_30
5 4 6 2 ga_17
etc.
[ dihedrals ] ; improper
; ai aj ak al fn gromos type
2 1 4 3 2 gi_1
4 2 5 6 2 gi_1
etc.
[ dihedrals ] ; proper
; ai aj ak al fn gromos type
7 6 4 2 1 gd_19
8 7 6 4 1 gd_17
19 8 7 6 1 gd_20
etc.
Best regards,
Martina
Pedro Alexandre Lapido Loureiro wrote:
>Hi!
>
>I think you forgot to write the "function" column in the [bonds], [angles],
>[dihedrals] and [impropers] items. Its value is "2" (except for [dihedrals] - in
>that case it`s "1"), but check the manual.
>
>Regards.
>
>
>
>
>
>>[ moleculetype ]
>> ;name nrexcl
>>DRG 3
>>[ atoms ]
>>; nr type resnr residue atom cgnr charge mass
>>typeB chargeB massB
>> 1 CH3 285 DRG CAO 1 0.000 15.035
>> 2 C 285 DRG CAM 1 0.380 12.011
>> 3 O 285 DRG OAN 1 -0.380 15.9994
>> 4 N 285 DRG NAL 2 -0.280 14.0067
>> 5 H 285 DRG HAB 2 0.280 1.008
>> 6 CH2 285 DRG CAK 3 0.000 14.027
>> 7 CH2 285 DRG CAJ 3 0.000 14.027
>> 8 C 285 DRG CAA 4 -0.140 12.011
>> 9 C 285 DRG CAC 4 0.000 12.011
>> 10 CR1 285 DRG CAF 5 0.000 13.019
>> 11 C 285 DRG CAH 5 0.100 12.011
>> 12 OA 285 DRG OAP 6 -0.100 15.9994
>> 13 CH3 285 DRG CAQ 6 0.000 15.035
>> 14 CR1 285 DRG CAI 7 0.000 13.019
>> 15 CR1 285 DRG CAG 7 0.000 13.019
>> 16 C 285 DRG CAE 8 0.000 12.011
>> 17 NR 285 DRG NAD 8 -0.050 14.0067
>> 18 H 285 DRG HAA 8 0.190 1.008
>> 19 CR1 285 DRG CAB 8 0.000 13.019
>>[ bonds ]
>> 1 2 gb_26
>> 2 3 gb_4
>> 2 4 gb_9
>> 4 5 gb_2
>> 4 6 gb_20
>> 6 7 gb_26
>> 7 8 gb_14
>> 8 19 gb_9
>> 8 9 gb_9
>> 19 17 gb_9
>> 17 18 gb_2
>> 17 16 gb_9
>> 16 9 gb_15
>> 9 10 gb_15
>> 10 11 gb_15
>> 11 14 gb_15
>> 14 15 gb_15
>> 15 16 gb_15
>> 11 12 gb_12
>> 12 13 gb_17
>> [ angles ]
>>; ai aj ak gromos type
>> 1 2 3 ga_29
>> 1 2 4 ga_18
>> 3 2 4 ga_32
>> 2 4 5 ga_31
>> 2 4 6 ga_30
>> 5 4 6 ga_17
>> 4 6 7 ga_12
>> 6 7 8 ga_14
>> 7 8 19 ga_36
>> 8 19 17 ga_6
>> 19 17 18 ga_35
>> 19 17 16 ga_6
>> 19 8 9 ga_6
>> 8 9 16 ga_6
>> 9 16 17 ga_6
>> 17 16 15 ga_38
>> 8 9 10 ga_38
>> 16 9 10 ga_26
>> 9 10 11 ga_26
>> 10 11 14 ga_26
>> 11 14 15 ga_26
>> 14 15 16 ga_26
>> 15 16 9 ga_26
>> 10 11 12 ga_18
>> 11 12 13 ga_11
>> 14 11 12 ga_18
>> [ impropers ]
>>; ai aj ak al gromos type
>> 2 1 4 3 gi_1
>> 4 2 5 6 gi_1
>> 8 19 9 7 gi_1
>> 9 8 16 10 gi_1
>> 11 14 12 10 gi_1
>> 16 9 15 17 gi_1
>> 17 16 18 19 gi_1
>> 8 9 16 17 gi_1
>> 9 16 17 19 gi_1
>> 16 17 19 8 gi_1
>> 17 19 8 9 gi_1
>> 19 8 9 16 gi_1
>> 9 10 11 14 gi_1
>> 10 11 14 15 gi_1
>> 11 14 15 16 gi_1
>> 14 15 16 9 gi_1
>> 15 16 9 10 gi_1
>> 16 9 10 11 gi_1
>>
>> [ dihedrals ]
>>; ai aj ak al gromos type
>> 1 2 4 6 gd_4
>> 7 6 4 2 gd_19
>> 8 7 6 4 gd_17
>> 19 8 7 6 gd_20
>> 10 11 12 13 gd_2
>>
>
>
>--
>Pedro Alexandre Lapido Loureiro
>Laboratório de Física Biológica
>Instituto de Biofísica
>UFRJ
>Brasil
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