[gmx-users] Re: problems running grompp with protein-ligand complex
Ragnarok sdf
fabracht1 at gmail.com
Tue Dec 2 13:33:30 CET 2008
Hello. I will try now to send part of my itp file and if another part
of the file is needed I will send it if requested.
Below are the emails that were already sent regarding my problem.
I hope I have not caused any incovenience.
Fabrício Bracht
" I am working with a protein-ligand complex in gromacs with ffamber99
forcefield. I was able to generate the topology file for my ligand
with acpypi. Was also able to insert the ligand coordinates into my
protein's coordinate file. Was also able to generate the water box
with genbox. The number of molecules all match, the ligand coordinates
are still there but grompp tells me that:
Fatal error: Found a second defaults directive, file "ligand.itp", line 5
I've checked wikigromacs, but the solution given there, to simply
erase the second default line does not suit me here. Once I do this, i
mean, go to my ligand.itp file and put a ; before my default section,
grompp does not recognize anymore that my ligand is there and gives
out another error line.
I would like some advice on the matter if possible.
Thank you in advance
Fabrício Bracht
>Well, it's not like grompp is recognizing you have a ligand there
>right now, is it? grompp doesn't reach the point where it realizes you
>don't seem to have a ligand. It seems there's something wrong with the
>topology. Better post ligand.itp, like Justin suggests, and also give
>the error which occurs when you do comment out the defaults line in
>the ligand topology.
>
>Cheers,
>
>Tsjerk "
Now, the actual itp file.
; M_E.top created by acpypi on Wed Nov 26 18:00:37 2008
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.8333
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon Amb
o o 0.00000 0.00000 A 2.95992e-01
8.78640e-01 ; 1.66 0.2100
c c 0.00000 0.00000 A 3.39967e-01
3.59824e-01 ; 1.91 0.0860
oh oh 0.00000 0.00000 A 3.06647e-01
8.80314e-01 ; 1.72 0.2104
ho ho 0.00000 0.00000 A 0.00000e+00
0.00000e+00 ; 0.00 0.0000
c3 c3 0.00000 0.00000 A 3.39967e-01
4.57730e-01 ; 1.91 0.1094
hc hc 0.00000 0.00000 A 2.64953e-01
6.56888e-02 ; 1.49 0.0157
c2 c2 0.00000 0.00000 A 3.39967e-01
3.59824e-01 ; 1.91 0.0860
ha ha 0.00000 0.00000 A 2.59964e-01
6.27600e-02 ; 1.46 0.0150
ce ce 0.00000 0.00000 A 3.39967e-01
3.59824e-01 ; 1.91 0.0860
cf cf 0.00000 0.00000 A 3.39967e-01
3.59824e-01 ; 1.91 0.0860
[ moleculetype ]
;name nrexcl
M_E 3
[ atoms ]
; nr type resi res atom cgnr charge mass typeB chargeB
1 o 1 M_E O49 1 -0.55230 16.00000 ; qtot -0.552
2 c 1 M_E C48 2 0.63200 12.01000 ; qtot 0.080
3 oh 1 M_E O50 3 -0.60900 16.00000 ; qtot -0.529
4 ho 1 M_E H51 4 0.44690 1.00800 ; qtot -0.082
5 c3 1 M_E C45 5 -0.12590 12.01000 ; qtot -0.208
6 hc 1 M_E H46 6 0.08080 1.00800 ; qtot -0.127
7 hc 1 M_E H47 7 0.08110 1.00800 ; qtot -0.046
8 c3 1 M_E C42 8 -0.07210 12.01000 ; qtot -0.118
9 hc 1 M_E H43 9 0.06640 1.00800 ; qtot -0.052
10 hc 1 M_E H44 10 0.05040 1.00800 ; qtot -0.002
11 c3 1 M_E C39 11 -0.05170 12.01000 ; qtot -0.053
12 hc 1 M_E H40 12 0.04490 1.00800 ; qtot -0.008
13 hc 1 M_E H41 13 0.05410 1.00800 ; qtot 0.046
14 c2 1 M_E C37 14 -0.16730 12.01000 ; qtot -0.122
15 ha 1 M_E H38 15 0.11950 1.00800 ; qtot -0.002
16 c2 1 M_E C35 16 -0.16710 12.01000 ; qtot -0.169
17 ha 1 M_E H36 17 0.11730 1.00800 ; qtot -0.052
18 c3 1 M_E C32 18 -0.04940 12.01000 ; qtot -0.101
19 hc 1 M_E H33 19 0.07250 1.00800 ; qtot -0.029
20 hc 1 M_E H34 20 0.06180 1.00800 ; qtot 0.033
21 c3 1 M_E C2 21 -0.00340 12.01000 ; qtot 0.030
22 hc 1 M_E H6 22 0.07250 1.00800 ; qtot 0.102
23 c2 1 M_E C1 23 -0.10390 12.01000 ; qtot -0.002
24 ha 1 M_E H8 24 0.14850 1.00800 ; qtot 0.147
25 ce 1 M_E C5 25 -0.25360 12.01000 ; qtot -0.107
26 ha 1 M_E H9 26 0.16130 1.00800 ; qtot 0.054
27 c 1 M_E C4 27 0.56070 12.01000 ; qtot 0.615
28 o 1 M_E O7 28 -0.52650 16.00000 ; qtot 0.089
29 ce 1 M_E C3 29 -0.21970 12.01000 ; qtot -0.131
30 cf 1 M_E C10 30 -0.04110 12.01000 ; qtot -0.172
31 ha 1 M_E H11 31 0.14510 1.00800 ; qtot -0.027
32 cf 1 M_E C12 32 -0.16880 12.01000 ; qtot -0.196
33 ha 1 M_E H13 33 0.12600 1.00800 ; qtot -0.070
34 c2 1 M_E C14 34 -0.12090 12.01000 ; qtot -0.191
35 ha 1 M_E H15 35 0.12220 1.00800 ; qtot -0.069
36 c3 1 M_E C16 36 -0.06070 12.01000 ; qtot -0.129
37 hc 1 M_E H17 37 0.05610 1.00800 ; qtot -0.073
38 hc 1 M_E H18 38 0.05520 1.00800 ; qtot -0.018
39 c3 1 M_E C19 39 -0.07610 12.01000 ; qtot -0.094
40 hc 1 M_E H20 40 0.04810 1.00800 ; qtot -0.046
41 hc 1 M_E H21 41 0.03740 1.00800 ; qtot -0.009
42 c3 1 M_E C22 42 -0.07850 12.01000 ; qtot -0.087
43 hc 1 M_E H23 43 0.04140 1.00800 ; qtot -0.046
44 hc 1 M_E H24 44 0.03920 1.00800 ; qtot -0.007
45 c3 1 M_E C25 45 -0.08090 12.01000 ; qtot -0.088
46 hc 1 M_E H26 46 0.03910 1.00800 ; qtot -0.048
47 hc 1 M_E H27 47 0.04220 1.00800 ; qtot -0.006
48 c3 1 M_E C28 48 -0.09280 12.01000 ; qtot -0.099
49 hc 1 M_E H29 49 0.03180 1.00800 ; qtot -0.067
50 hc 1 M_E H30 50 0.03440 1.00800 ; qtot -0.033
51 hc 1 M_E H31 51 0.03280 1.00800 ; qtot -0.000
[ bonds ]
; ai aj funct r k
3 4 1 9.7400e-02 3.0928e+05 ; O50 - H51
(more text not sent)
[ pairs ]
; ai aj funct
6 9 1 ; H46 - H43
(more text not sent)
[ angles ]
; ai aj ak funct theta cth
2 3 4 1 1.0737e+02 4.2844e+02 ; C48 - O50
- H51
(more text not sent)
[ dihedrals ] ; propers
; treated as RBs in GROMACS to use combine multiple AMBER torsions per quartet
; i j k l func C0 C1 C2 C3 C4 C5
1 2 3 4 3 27.19600 -7.94960 -19.24640 0.00000
0.00000 0.00000 ; O49- C48- O50- H51
(more text not sent)
[ dihedrals ] ; impropers
; treated as propers in GROMACS to use correct AMBER analytical function
; i j k l func phase kd pn
16 11 14 15 1 180.00 4.60240 2 ; C35- C39- C37- H38
(more text not sent)
[ system ]
M_E
[ molecules ]
; Compound nmols
M_E 1
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