[gmx-users] mdrun error
محمد گره گشا
m.gerehgosha at gmail.com
Tue Dec 22 07:50:50 CET 2015
Dear all
I am a beginner in MD simulation using OPLSA force field in Gromacs . I
prepared ligand-protein complex step by step:
1- I build topology and gro file of protein
2- Add itp and gro file of ligand to it. I build them by
http://erg.biophys.msu.ru/tpp/ and PRDRUG , respectively.( I don't know,
my gro file is correct or not because I buld it PRDRUG.)
3- Partial charge atoms of ligand were calculated using Goussian.
In this step, there is an error: the sum of the two largest charge group
radii is larger than rlist-rvdw/rcoulomb
Would you please help have can I solve it?
I add itp and partial charge to this message.
; LIG - topology generator
; created by Erg Research Group
; MSU, Biology Faculty, Department of Biophysics
; ----------------------------------------------
; Topology was prepared for use with the forcefield: <ffoplsaa.itp>
[ moleculetype ]
LIG 3
; Force constant parameters
#define dfLIG_bon_1 1 0.140 3.92e+05 ;1
#define dfLIG_bon_3 1 0.136 3.77e+05 ;1
#define dfLIG_bon_5 1 0.136 3.77e+05 ;1
#define dfLIG_bon_7 1 0.108 3.07e+05 ;1
#define dfLIG_bon_9 1 0.140 3.92e+05 ;1
#define dfLIG_bon_15 1 0.134 4.04e+05 ;1
#define dfLIG_bon_17 1 0.134 4.04e+05 ;1
#define dfLIG_bon_18 1 0.151 2.65e+05 ;1
#define dfLIG_bon_20 1 0.109 2.85e+05 ;1
#define dfLIG_bon_33 1 0.141 2.68e+05 ;1
#define dfLIG_ang_1 1 120.0 527.2 ;2
#define dfLIG_ang_2 1 120.0 585.8 ;2
#define dfLIG_ang_8 1 120.0 292.9 ;2
#define dfLIG_ang_22 1 124.0 585.8 ;2
#define dfLIG_ang_24 1 116.0 292.9 ;2
#define dfLIG_ang_27 1 116.0 585.8 ;2
#define dfLIG_ang_28 1 117.0 585.8 ;2
#define dfLIG_ang_29 1 109.5 334.7 ;2
#define dfLIG_ang_30 1 109.5 292.9 ;2
#define dfLIG_ang_34 1 107.8 276.1 ;2
#define dfLIG_ang_53 1 111.0 627.6 ;2
#define dfLIG_dih_1 3 +30.3 +0.0 -30.3 +0.0 +0.0 +0.0 ;3
#define dfLIG_dih_9 3 +12.6 +0.0 -12.6 +0.0 +0.0 +0.0 ;3
#define dfLIG_dih_16 3 +12.6 +0.0 -12.6 +0.0 +0.0 +0.0 ;3
#define dfLIG_dih_45 3 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 ;3
#define dfLIG_dih_85 3 +1.6 +4.8 +0.0 -6.4 +0.0 +0.0 ;3
[ atoms ]
1 opls_199 1 LIG CAA 1 0.179016 12.011000 ; C(O,Me): anisole
2 opls_199 1 LIG CAB 2 0.076137 12.011000 ; C(O,Me): anisole
3 opls_145 1 LIG CAC 3 -0.190807 12.011000 ; Benzene C - 12
site JACS,112,4768-90. Use #145B for biphenyl
4 opls_523 1 LIG CAD 4 0.066027 12.011000 ; C3 in pyridine
for
5 opls_522 1 LIG CAE 5 -0.114338 12.011000 ; C2 in pyridine
charges
6 opls_145 1 LIG CAF 6 -0.161633 12.011000 ; Benzene C - 12
site JACS,112,4768-90. Use #145B for biphenyl
7 opls_522 1 LIG CAI 7 0.235355 12.011000 ; C2 in pyridine
charges
8 opls_521 1 LIG CAG 8 -0.255026 12.011000 ; C1 in pyridine
CHELPG
9 opls_521 1 LIG CAH 9 0.040392 12.011000 ; C1 in pyridine
CHELPG
10 opls_520 1 LIG NAJ 10 -0.352241 14.006700 ; N in pyridine
6-31G*
11 opls_136 1 LIG CAK 11 -0.312125 12.011000 ; alkane CH2
12 opls_145 1 LIG CAL 12 0.097277 12.011000 ; Benzene C - 12
site JACS,112,4768-90. Use #145B for biphenyl
13 opls_145 1 LIG CAM 13 -0.280318 12.011000 ; Benzene C - 12
site JACS,112,4768-90. Use #145B for biphenyl
14 opls_199 1 LIG CAU 14 -0.215985 12.011000 ; C(O,Me): anisole
15 opls_199 1 LIG CAT 15 -0.213602 12.011000 ; C(O,Me): anisole
16 opls_145 1 LIG CAP 16 -0.184387 12.011000 ; Benzene C - 12
site JACS,112,4768-90. Use #145B for biphenyl
17 opls_145 1 LIG CAQ 17 -0.224424 12.011000 ; Benzene C - 12
site JACS,112,4768-90. Use #145B for biphenyl
18 opls_179 1 LIG OAV 18 -0.342419 15.999400 ; O: anisole
19 opls_179 1 LIG OAW 19 -0.333900 15.999400 ; O: anisole
20 opls_181 1 LIG CAX 20 -0.212853 12.011000 ; C(H3OR): methyl
ether
21 opls_181 1 LIG CAY 21 -0.228460 12.011000 ; C(H3OR): methyl
ether
22 opls_179 1 LIG OAS 22 -0.355106 15.999400 ; O: anisole
23 opls_179 1 LIG OAR 23 -0.367769 15.999400 ; O: anisole
24 opls_181 1 LIG CAO 24 0.206705 12.011000 ; C(H3OR): methyl
ether
25 opls_181 1 LIG CAN 25 0.183982 12.011000 ; C(H3OR): methyl
ether
26 opls_146 1 LIG HAC 3 0.175586 1.008000 ; Benzene H - 12
site.
27 opls_146 1 LIG HAF 6 0.158419 1.008000 ; Benzene H - 12
site.
28 opls_525 1 LIG HAH 7 0.158955 1.008000 ; H2 in pyridine
29 opls_524 1 LIG HAG 8 0.166532 1.008000 ; H1 in pyridine
520-619
30 opls_140 1 LIG HAK 11 0.168958 1.008000 ; alkane H.
31 opls_140 1 LIG HAL 11 0.156734 1.008000 ; alkane H.
32 opls_146 1 LIG HAM 13 0.170382 1.008000 ; Benzene H - 12
site.
33 opls_146 1 LIG HAP 16 0.152440 1.008000 ; Benzene H - 12
site.
34 opls_146 1 LIG HAQ 17 0.172579 1.008000 ; Benzene H - 12
site.
35 opls_185 1 LIG HAZ 20 0.151995 1.008000 ; H(COR): alpha H
ether
36 opls_185 1 LIG HA0 20 0.176774 1.008000 ; H(COR): alpha H
ether
37 opls_185 1 LIG HA1 20 0.156027 1.008000 ; H(COR): alpha H
ether
38 opls_185 1 LIG HA3 21 0.136723 1.008000 ; H(COR): alpha H
ether
39 opls_185 1 LIG HA4 21 0.133227 1.008000 ; H(COR): alpha H
ether
40 opls_185 1 LIG HA2 21 0.150323 1.008000 ; H(COR): alpha H
ether
41 opls_185 1 LIG HAX 24 0.134730 1.008000 ; H(COR): alpha H
ether
42 opls_185 1 LIG HAY 24 0.134489 1.008000 ; H(COR): alpha H
ether
43 opls_185 1 LIG HAW 24 0.144540 1.008000 ; H(COR): alpha H
ether
44 opls_185 1 LIG HAU 25 0.173081 1.008000 ; H(COR): alpha H
ether
45 opls_185 1 LIG HAV 25 0.153101 1.008000 ; H(COR): alpha H
ether
46 opls_185 1 LIG HAT 25 0.135178 1.008000 ; H(COR): alpha H
ether
[ bonds ]
1 2 dfLIG_bon_1
1 3 dfLIG_bon_1
2 6 dfLIG_bon_1
3 4 dfLIG_bon_1
4 5 dfLIG_bon_1
4 7 dfLIG_bon_1
5 6 dfLIG_bon_1
5 9 dfLIG_bon_1
7 8 dfLIG_bon_1
12 13 dfLIG_bon_1
12 16 dfLIG_bon_1
13 14 dfLIG_bon_1
14 15 dfLIG_bon_1
15 17 dfLIG_bon_1
16 17 dfLIG_bon_1
15 19 dfLIG_bon_3
1 22 dfLIG_bon_3
2 23 dfLIG_bon_3
14 18 dfLIG_bon_3
3 26 dfLIG_bon_7
6 27 dfLIG_bon_7
7 28 dfLIG_bon_7
8 29 dfLIG_bon_7
13 32 dfLIG_bon_7
16 33 dfLIG_bon_7
17 34 dfLIG_bon_7
8 10 dfLIG_bon_15
9 10 dfLIG_bon_15
9 11 dfLIG_bon_18
11 12 dfLIG_bon_18
11 30 dfLIG_bon_20
11 31 dfLIG_bon_20
20 35 dfLIG_bon_20
20 36 dfLIG_bon_20
20 37 dfLIG_bon_20
21 38 dfLIG_bon_20
21 39 dfLIG_bon_20
21 40 dfLIG_bon_20
24 41 dfLIG_bon_20
24 42 dfLIG_bon_20
24 43 dfLIG_bon_20
25 44 dfLIG_bon_20
25 45 dfLIG_bon_20
25 46 dfLIG_bon_20
18 20 dfLIG_bon_33
19 21 dfLIG_bon_33
22 24 dfLIG_bon_33
23 25 dfLIG_bon_33
[ pairs ]
10 12 1
3 1 1
3 1 1
22 1 1
22 1 1
2 1 1
2 1 1
22 1 1
22 1 1
2 1 1
3 1 1
1 2 1
1 2 1
23 2 1
23 2 1
1 2 1
6 2 1
1 3 1
1 3 1
26 3 1
26 3 1
3 4 1
3 4 1
7 4 1
7 4 1
3 4 1
3 4 1
5 4 1
5 4 1
4 5 1
4 5 1
9 5 1
9 5 1
4 5 1
4 5 1
6 5 1
6 5 1
4 7 1
4 7 1
28 7 1
28 7 1
7 8 1
29 8 1
5 9 1
11 9 1
5 9 1
5 9 1
5 9 1
10 9 1
10 9 1
10 9 1
9 11 1
9 11 1
30 11 1
30 11 1
31 11 1
31 11 1
11 12 1
11 12 1
16 12 1
16 12 1
11 12 1
11 12 1
13 12 1
13 12 1
12 13 1
12 13 1
32 13 1
32 13 1
13 14 1
13 14 1
18 14 1
18 14 1
13 14 1
15 14 1
14 15 1
14 15 1
19 15 1
19 15 1
14 15 1
17 15 1
12 16 1
12 16 1
33 16 1
33 16 1
14 18 1
14 18 1
14 18 1
15 19 1
15 19 1
15 19 1
1 22 1
1 22 1
1 22 1
2 23 1
2 23 1
2 23 1
[ angles ]
2 1 3 dfLIG_ang_1
1 2 6 dfLIG_ang_1
1 3 4 dfLIG_ang_1
3 4 5 dfLIG_ang_1
3 4 7 dfLIG_ang_1
5 4 7 dfLIG_ang_1
4 5 6 dfLIG_ang_1
4 5 9 dfLIG_ang_1
6 5 9 dfLIG_ang_1
2 6 5 dfLIG_ang_1
4 7 8 dfLIG_ang_1
13 12 16 dfLIG_ang_1
12 13 14 dfLIG_ang_1
13 14 15 dfLIG_ang_1
14 15 17 dfLIG_ang_1
12 16 17 dfLIG_ang_1
15 17 16 dfLIG_ang_1
2 1 22 dfLIG_ang_2
3 1 22 dfLIG_ang_2
1 2 23 dfLIG_ang_2
6 2 23 dfLIG_ang_2
5 9 11 dfLIG_ang_2
11 12 13 dfLIG_ang_2
11 12 16 dfLIG_ang_2
13 14 18 dfLIG_ang_2
15 14 18 dfLIG_ang_2
14 15 19 dfLIG_ang_2
17 15 19 dfLIG_ang_2
1 3 26 dfLIG_ang_8
4 3 26 dfLIG_ang_8
2 6 27 dfLIG_ang_8
5 6 27 dfLIG_ang_8
4 7 28 dfLIG_ang_8
8 7 28 dfLIG_ang_8
7 8 29 dfLIG_ang_8
12 13 32 dfLIG_ang_8
14 13 32 dfLIG_ang_8
12 16 33 dfLIG_ang_8
17 16 33 dfLIG_ang_8
15 17 34 dfLIG_ang_8
16 17 34 dfLIG_ang_8
7 8 10 dfLIG_ang_22
5 9 10 dfLIG_ang_22
10 8 29 dfLIG_ang_24
10 9 11 dfLIG_ang_27
8 10 9 dfLIG_ang_28
9 11 12 dfLIG_ang_29
9 11 30 dfLIG_ang_30
9 11 31 dfLIG_ang_30
12 11 30 dfLIG_ang_30
12 11 31 dfLIG_ang_30
18 20 35 dfLIG_ang_30
18 20 36 dfLIG_ang_30
18 20 37 dfLIG_ang_30
19 21 38 dfLIG_ang_30
19 21 39 dfLIG_ang_30
19 21 40 dfLIG_ang_30
22 24 41 dfLIG_ang_30
22 24 42 dfLIG_ang_30
22 24 43 dfLIG_ang_30
23 25 44 dfLIG_ang_30
23 25 45 dfLIG_ang_30
23 25 46 dfLIG_ang_30
30 11 31 dfLIG_ang_34
35 20 36 dfLIG_ang_34
35 20 37 dfLIG_ang_34
36 20 37 dfLIG_ang_34
38 21 39 dfLIG_ang_34
38 21 40 dfLIG_ang_34
39 21 40 dfLIG_ang_34
41 24 42 dfLIG_ang_34
41 24 43 dfLIG_ang_34
42 24 43 dfLIG_ang_34
44 25 45 dfLIG_ang_34
44 25 46 dfLIG_ang_34
45 25 46 dfLIG_ang_34
14 18 20 dfLIG_ang_53
15 19 21 dfLIG_ang_53
1 22 24 dfLIG_ang_53
2 23 25 dfLIG_ang_53
[ dihedrals ]
3 1 2 6 dfLIG_dih_1
3 1 2 23 dfLIG_dih_1
22 1 2 6 dfLIG_dih_1
22 1 2 23 dfLIG_dih_1
2 1 3 4 dfLIG_dih_1
2 1 3 26 dfLIG_dih_1
22 1 3 4 dfLIG_dih_1
22 1 3 26 dfLIG_dih_1
1 2 6 5 dfLIG_dih_1
1 2 6 27 dfLIG_dih_1
23 2 6 5 dfLIG_dih_1
23 2 6 27 dfLIG_dih_1
1 3 4 5 dfLIG_dih_1
1 3 4 7 dfLIG_dih_1
26 3 4 5 dfLIG_dih_1
26 3 4 7 dfLIG_dih_1
3 4 5 6 dfLIG_dih_1
3 4 5 9 dfLIG_dih_1
7 4 5 6 dfLIG_dih_1
7 4 5 9 dfLIG_dih_1
3 4 7 8 dfLIG_dih_1
3 4 7 28 dfLIG_dih_1
5 4 7 8 dfLIG_dih_1
5 4 7 28 dfLIG_dih_1
4 5 6 2 dfLIG_dih_1
4 5 6 27 dfLIG_dih_1
9 5 6 2 dfLIG_dih_1
9 5 6 27 dfLIG_dih_1
4 5 9 10 dfLIG_dih_1
4 5 9 11 dfLIG_dih_1
6 5 9 10 dfLIG_dih_1
6 5 9 11 dfLIG_dih_1
4 7 8 10 dfLIG_dih_1
4 7 8 29 dfLIG_dih_1
28 7 8 10 dfLIG_dih_1
28 7 8 29 dfLIG_dih_1
7 8 10 9 dfLIG_dih_1
29 8 10 9 dfLIG_dih_1
5 9 10 8 dfLIG_dih_1
11 9 10 8 dfLIG_dih_1
11 12 13 14 dfLIG_dih_1
11 12 13 32 dfLIG_dih_1
16 12 13 14 dfLIG_dih_1
16 12 13 32 dfLIG_dih_1
11 12 16 17 dfLIG_dih_1
11 12 16 33 dfLIG_dih_1
13 12 16 17 dfLIG_dih_1
13 12 16 33 dfLIG_dih_1
12 13 14 15 dfLIG_dih_1
12 13 14 18 dfLIG_dih_1
32 13 14 15 dfLIG_dih_1
32 13 14 18 dfLIG_dih_1
13 14 15 17 dfLIG_dih_1
13 14 15 19 dfLIG_dih_1
18 14 15 17 dfLIG_dih_1
18 14 15 19 dfLIG_dih_1
14 15 17 16 dfLIG_dih_1
14 15 17 34 dfLIG_dih_1
19 15 17 16 dfLIG_dih_1
19 15 17 34 dfLIG_dih_1
12 16 17 15 dfLIG_dih_1
12 16 17 34 dfLIG_dih_1
33 16 17 15 dfLIG_dih_1
33 16 17 34 dfLIG_dih_1
2 1 22 24 dfLIG_dih_1
3 1 22 24 dfLIG_dih_1
1 2 23 25 dfLIG_dih_1
6 2 23 25 dfLIG_dih_1
13 14 18 20 dfLIG_dih_1
15 14 18 20 dfLIG_dih_1
14 15 19 21 dfLIG_dih_1
17 15 19 21 dfLIG_dih_1
5 9 11 12 dfLIG_dih_1
5 9 11 30 dfLIG_dih_1
5 9 11 31 dfLIG_dih_1
10 9 11 30 dfLIG_dih_1
10 9 11 31 dfLIG_dih_1
9 11 12 13 dfLIG_dih_1
9 11 12 16 dfLIG_dih_1
30 11 12 13 dfLIG_dih_1
30 11 12 16 dfLIG_dih_1
31 11 12 13 dfLIG_dih_1
31 11 12 16 dfLIG_dih_1
10 9 11 12 dfLIG_dih_1
14 18 20 35 dfLIG_dih_1
14 18 20 36 dfLIG_dih_1
14 18 20 37 dfLIG_dih_1
15 19 21 38 dfLIG_dih_1
15 19 21 39 dfLIG_dih_1
15 19 21 40 dfLIG_dih_1
1 22 24 41 dfLIG_dih_1
1 22 24 42 dfLIG_dih_1
1 22 24 43 dfLIG_dih_1
2 23 25 44 dfLIG_dih_1
2 23 25 45 dfLIG_dih_1
2 23 25 46 dfLIG_dih_1
Best
On Tue, Dec 22, 2015 at 9:06 AM, محمد گره گشا <m.gerehgosha at gmail.com>
wrote:
> Dears all
> Hi
> we run a MD simulation. but when we using mdrun command to energy
> minimization encountered this message: "killed" and No error appears.
> so anyone can help please?
> thank you
>
> On Mon, Dec 21, 2015 at 10:08 AM, محمد گره گشا <m.gerehgosha at gmail.com>
> wrote:
>
>> Hi all dears
>> We run a MD simulation. and when we use mdrun command to energy
>> minimization face this message: 'Killed' and no error.
>> anyone can help we please?
>> thanks
>>
>
>
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