[gmx-users] Silly question?
Sergio Manzetti
sergio.manzetti at vestforsk.no
Wed Dec 22 19:39:09 CET 2010
Thanks Justin: here is the top:
[ moleculetype ]
; Name nrexcl
BZP 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 opls_648 1 BZP C1 1 0 12.0107 ;
qtot 0
2 opls_648 1 BZP C2 2 0 12.0107 ;
qtot 0
3 opls_648 1 BZP C3 3 0 12.0107 ;
qtot 0
4 opls_648 1 BZP C4 4 0 12.0107 ;
qtot 0
5 opls_145 1 BZP C5 5 0 12.0107 ;
qtot 0
6 opls_146 1 BZP 1H5 5 0 1.0079
; qtot 0
7 opls_145 1 BZP C6 6 0 12.0107 ;
qtot 0
8 opls_146 1 BZP 1H6 6 0 1.0079
; qtot 0
9 opls_145 1 BZP C7 7 0 12.0107 ;
qtot 0
10 opls_146 1 BZP 1H7 7 0 1.0079
; qtot 0
11 opls_145 1 BZP C8 8 0 12.0107 ;
qtot 0
12 opls_146 1 BZP 1H8 8 0 1.0079
; qtot 0
13 opls_648 1 BZP C9 9 0 12.0107 ;
qtot 0
14 opls_145 1 BZP C10 10 0 12.0107 ;
qtot 0
15 opls_146 1 BZP 1H10 10 0 1.0079
; qtot 0
16 opls_648 1 BZP C11 11 0 12.0107 ;
qtot 0
17 opls_145 1 BZP C12 12 0 12.0107 ;
qtot 0
18 opls_146 1 BZP 1H12 12 0 1.0079
; qtot 0
19 opls_145 1 BZP C13 13 0 12.0107 ;
qtot 0
20 opls_146 1 BZP 1H13 13 0 1.0079
; qtot 0
21 opls_648 1 BZP C14 14 0 12.0107 ;
qtot 0
22 opls_145 1 BZP C15 15 0 12.0107 ;
qtot 0
23 opls_146 1 BZP 1H15 15 0 1.0079
; qtot 0
24 opls_145 1 BZP C16 16 0 12.0107 ;
qtot 0
25 opls_146 1 BZP 1H16 16 0 1.0079
; qtot 0
26 opls_145 1 BZP C17 17 0 12.0107 ;
qtot 0
27 opls_146 1 BZP 1H17 17 0 1.0079
; qtot 0
28 opls_648 1 BZP C18 18 0 12.0107 ;
qtot 0
29 opls_145 1 BZP C19 19 0 12.0107 ;
qtot 0
30 opls_146 1 BZP 1H19 19 0 1.0079
; qtot 0
31 opls_145 1 BZP C20 20 0 12.0107 ;
qtot 0
32 opls_146 1 BZP 1H20 20 0 1.0079
; qtot 0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05
1 21 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05
1 28 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05
2 3 1 1.430000e-01 4.000000e+05 1.430000e-01 4.000000e+05
2 16 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05
3 4 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05
3 31 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05
4 5 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05
4 13 1 1.430000e-01 4.000000e+05 1.430000e-01 4.000000e+05
5 6 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05
5 7 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05
7 8 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05
7 9 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05
9 10 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05
9 11 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05
11 12 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05
11 13 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05
13 14 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05
14 15 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05
14 16 1 1.390000e-01 4.000000e+05 1.390000e-01 4.000000e+05
16 17 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05
17 18 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05
17 19 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05
19 20 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05
19 21 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05
21 22 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05
22 23 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05
22 24 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05
24 25 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05
24 26 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05
26 27 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05
26 28 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05
28 29 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05
29 30 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05
29 31 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05
31 32 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05
[ exclusions ]
; i excluded from i
1 2 21 28
2 1 3 16
3 2 4 31
4 3 5 13
5 4 6 7
6 5
7 5 8 9
8 7
9 7 10 11
10 9
11 9 12 13
12 11
13 4 11 14
14 13 15 16
15 14
16 2 14 17
17 16 18 19
18 17
19 17 20 21
20 19
21 1 19 22
22 21 23 24
23 22
24 22 25 26
25 24
26 24 27 28
27 26
28 1 26 29
29 28 30 31
30 29
31 3 29 32
32 31
[ angles ]
; ai aj ak funct c0 c1 c2
c3
2 1 21 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
2 1 28 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
21 1 28 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
1 2 3 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
1 2 16 1 1.190000e+02 4.000000e+02 1.190000e+02
4.000000e+02
3 2 16 1 1.210000e+02 4.000000e+02 1.210000e+02
4.000000e+02
2 3 4 1 1.190000e+02 4.000000e+02 1.190000e+02
4.000000e+02
2 3 31 1 1.180000e+02 4.000000e+02 1.180000e+02
4.000000e+02
4 3 31 1 1.230000e+02 4.000000e+02 1.230000e+02
4.000000e+02
3 4 5 1 1.220000e+02 4.000000e+02 1.220000e+02
4.000000e+02
3 4 13 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
5 4 13 1 1.180000e+02 4.000000e+02 1.180000e+02
4.000000e+02
4 5 6 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
4 5 7 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
6 5 7 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
5 7 8 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
5 7 9 1 1.210000e+02 4.000000e+02 1.210000e+02
4.000000e+02
8 7 9 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
7 9 10 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
7 9 11 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
10 9 11 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
9 11 12 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
9 11 13 1 1.190000e+02 4.000000e+02 1.190000e+02
4.000000e+02
12 11 13 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
4 13 11 1 1.210000e+02 4.000000e+02 1.210000e+02
4.000000e+02
4 13 14 1 1.210000e+02 4.000000e+02 1.210000e+02
4.000000e+02
11 13 14 1 1.180000e+02 4.000000e+02 1.180000e+02
4.000000e+02
13 14 15 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
13 14 16 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
15 14 16 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
2 16 14 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
2 16 17 1 1.210000e+02 4.000000e+02 1.210000e+02
4.000000e+02
14 16 17 1 1.190000e+02 4.000000e+02 1.190000e+02
4.000000e+02
16 17 18 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
16 17 19 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
18 17 19 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
17 19 20 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
17 19 21 1 1.190000e+02 4.000000e+02 1.190000e+02
4.000000e+02
20 19 21 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
1 21 19 1 1.210000e+02 4.000000e+02 1.210000e+02
4.000000e+02
1 21 22 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
19 21 22 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
21 22 23 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
21 22 24 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
23 22 24 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
22 24 25 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
22 24 26 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
25 24 26 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
24 26 27 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
24 26 28 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
27 26 28 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
1 28 26 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
1 28 29 1 1.210000e+02 4.000000e+02 1.210000e+02
4.000000e+02
26 28 29 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
28 29 30 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
28 29 31 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
30 29 31 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
3 31 29 1 1.220000e+02 4.000000e+02 1.220000e+02
4.000000e+02
3 31 32 1 1.190000e+02 4.000000e+02 1.190000e+02
4.000000e+02
29 31 32 1 1.190000e+02 4.000000e+02 1.190000e+02
4.000000e+02
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3
1 2 21 28 1 1.800000e+02 5.000000e+00 1.800000e+02
5.000000e+00
2 1 3 16 1 1.800000e+02 5.000000e+00 1.800000e+02
5.000000e+00
3 2 4 31 1 1.800000e+02 5.000000e+00 1.800000e+02
5.000000e+00
4 3 5 13 1 1.800000e+02 5.000000e+00 1.800000e+02
5.000000e+00
5 4 6 7 1 1.800000e+02 5.000000e+00 1.800000e+02
5.000000e+00
7 5 8 9 1 1.800000e+02 5.000000e+00 1.800000e+02
5.000000e+00
9 7 10 11 1 1.800000e+02 5.000000e+00 1.800000e+02
5.000000e+00
11 9 12 13 1 1.800000e+02 5.000000e+00 1.800000e+02
5.000000e+00
13 4 11 14 1 1.800000e+02 5.000000e+00 1.800000e+02
5.000000e+00
14 13 15 16 1 1.800000e+02 5.000000e+00 1.800000e+02
5.000000e+00
16 2 14 17 1 1.800000e+02 5.000000e+00 1.800000e+02
5.000000e+00
17 16 18 19 1 1.800000e+02 5.000000e+00 1.800000e+02
5.000000e+00
19 17 20 21 1 1.800000e+02 5.000000e+00 1.800000e+02
5.000000e+00
21 1 19 22 1 1.800000e+02 5.000000e+00 1.800000e+02
5.000000e+00
22 21 23 24 1 1.800000e+02 5.000000e+00 1.800000e+02
5.000000e+00
24 22 25 26 1 1.800000e+02 5.000000e+00 1.800000e+02
5.000000e+00
26 24 27 28 1 1.800000e+02 5.000000e+00 1.800000e+02
5.000000e+00
28 1 26 29 1 1.800000e+02 5.000000e+00 1.800000e+02
5.000000e+00
29 28 30 31 1 1.800000e+02 5.000000e+00 1.800000e+02
5.000000e+00
31 3 29 32 1 1.800000e+02 5.000000e+00 1.800000e+02
5.000000e+00
On Wed, Dec 22, 2010 at 7:36 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Sergio Manzetti wrote:
>
>>
>>
>>
>> I am trying to grompp a molecule, but get the same error again:
>>
>> Program grompp, VERSION 4.5.1
>> Source code file: topio.c, line: 654
>>
>> Fatal error:
>> Syntax error - File bzp.itp, line 1
>> Last line read:
>> '[ moleculetype ]'
>> Invalid order for directive moleculetype
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
>> Can any help?
>>
>>
> Something in your topology is out of order. See Chapter 5 of the manual
> for the proper order. Either you've #included one moleculetype inside
> another, or you've done it before the force field has defined. Either way,
> if you want further assistance, you'll have to post some relevant snapshots
> of your topology.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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