Thanks Justin: here is the top:<br><br><br>[ moleculetype ]<br>; Name nrexcl<br>BZP 2<br><br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass typeB chargeB massB<br>
1 opls_648 1 BZP C1 1 0 12.0107 ; qtot 0<br> 2 opls_648 1 BZP C2 2 0 12.0107 ; qtot 0<br> 3 opls_648 1 BZP C3 3 0 12.0107 ; qtot 0<br>
4 opls_648 1 BZP C4 4 0 12.0107 ; qtot 0<br> 5 opls_145 1 BZP C5 5 0 12.0107 ; qtot 0<br> 6 opls_146 1 BZP 1H5 5 0 1.0079 ; qtot 0<br>
7 opls_145 1 BZP C6 6 0 12.0107 ; qtot 0<br> 8 opls_146 1 BZP 1H6 6 0 1.0079 ; qtot 0<br> 9 opls_145 1 BZP C7 7 0 12.0107 ; qtot 0<br>
10 opls_146 1 BZP 1H7 7 0 1.0079 ; qtot 0<br> 11 opls_145 1 BZP C8 8 0 12.0107 ; qtot 0<br> 12 opls_146 1 BZP 1H8 8 0 1.0079 ; qtot 0<br>
13 opls_648 1 BZP C9 9 0 12.0107 ; qtot 0<br> 14 opls_145 1 BZP C10 10 0 12.0107 ; qtot 0<br> 15 opls_146 1 BZP 1H10 10 0 1.0079 ; qtot 0<br>
16 opls_648 1 BZP C11 11 0 12.0107 ; qtot 0<br> 17 opls_145 1 BZP C12 12 0 12.0107 ; qtot 0<br> 18 opls_146 1 BZP 1H12 12 0 1.0079 ; qtot 0<br>
19 opls_145 1 BZP C13 13 0 12.0107 ; qtot 0<br> 20 opls_146 1 BZP 1H13 13 0 1.0079 ; qtot 0<br> 21 opls_648 1 BZP C14 14 0 12.0107 ; qtot 0<br>
22 opls_145 1 BZP C15 15 0 12.0107 ; qtot 0<br> 23 opls_146 1 BZP 1H15 15 0 1.0079 ; qtot 0<br> 24 opls_145 1 BZP C16 16 0 12.0107 ; qtot 0<br>
25 opls_146 1 BZP 1H16 16 0 1.0079 ; qtot 0<br> 26 opls_145 1 BZP C17 17 0 12.0107 ; qtot 0<br> 27 opls_146 1 BZP 1H17 17 0 1.0079 ; qtot 0<br>
28 opls_648 1 BZP C18 18 0 12.0107 ; qtot 0<br> 29 opls_145 1 BZP C19 19 0 12.0107 ; qtot 0<br> 30 opls_146 1 BZP 1H19 19 0 1.0079 ; qtot 0<br>
31 opls_145 1 BZP C20 20 0 12.0107 ; qtot 0<br> 32 opls_146 1 BZP 1H20 20 0 1.0079 ; qtot 0<br><br>[ bonds ]<br>; ai aj funct c0 c1 c2 c3<br>
1 2 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05 <br> 1 21 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05 <br> 1 28 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05 <br>
2 3 1 1.430000e-01 4.000000e+05 1.430000e-01 4.000000e+05 <br> 2 16 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05 <br> 3 4 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05 <br>
3 31 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05 <br> 4 5 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05 <br> 4 13 1 1.430000e-01 4.000000e+05 1.430000e-01 4.000000e+05 <br>
5 6 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 <br> 5 7 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05 <br> 7 8 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 <br>
7 9 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05 <br> 9 10 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 <br> 9 11 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05 <br>
11 12 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 <br> 11 13 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05 <br> 13 14 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05 <br>
14 15 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 <br> 14 16 1 1.390000e-01 4.000000e+05 1.390000e-01 4.000000e+05 <br> 16 17 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05 <br>
17 18 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 <br> 17 19 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05 <br> 19 20 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 <br>
19 21 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05 <br> 21 22 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05 <br> 22 23 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 <br>
22 24 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05 <br> 24 25 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 <br> 24 26 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05 <br>
26 27 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 <br> 26 28 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05 <br> 28 29 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05 <br>
29 30 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 <br> 29 31 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05 <br> 31 32 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 <br>
<br>[ exclusions ]<br>; i excluded from i<br> 1 2 21 28<br> 2 1 3 16<br> 3 2 4 31<br> 4 3 5 13<br> 5 4 6 7<br> 6 5<br> 7 5 8 9<br>
8 7<br> 9 7 10 11<br> 10 9<br> 11 9 12 13<br> 12 11<br> 13 4 11 14<br> 14 13 15 16<br> 15 14<br> 16 2 14 17<br> 17 16 18 19<br>
18 17<br> 19 17 20 21<br> 20 19<br> 21 1 19 22<br> 22 21 23 24<br> 23 22<br> 24 22 25 26<br> 25 24<br> 26 24 27 28<br> 27 26<br>
28 1 26 29<br> 29 28 30 31<br> 30 29<br> 31 3 29 32<br> 32 31<br><br>[ angles ]<br>; ai aj ak funct c0 c1 c2 c3<br>
2 1 21 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 2 1 28 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 21 1 28 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br>
1 2 3 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 1 2 16 1 1.190000e+02 4.000000e+02 1.190000e+02 4.000000e+02 <br> 3 2 16 1 1.210000e+02 4.000000e+02 1.210000e+02 4.000000e+02 <br>
2 3 4 1 1.190000e+02 4.000000e+02 1.190000e+02 4.000000e+02 <br> 2 3 31 1 1.180000e+02 4.000000e+02 1.180000e+02 4.000000e+02 <br> 4 3 31 1 1.230000e+02 4.000000e+02 1.230000e+02 4.000000e+02 <br>
3 4 5 1 1.220000e+02 4.000000e+02 1.220000e+02 4.000000e+02 <br> 3 4 13 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 5 4 13 1 1.180000e+02 4.000000e+02 1.180000e+02 4.000000e+02 <br>
4 5 6 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 4 5 7 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 6 5 7 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br>
5 7 8 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 5 7 9 1 1.210000e+02 4.000000e+02 1.210000e+02 4.000000e+02 <br> 8 7 9 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br>
7 9 10 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 7 9 11 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 10 9 11 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br>
9 11 12 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 9 11 13 1 1.190000e+02 4.000000e+02 1.190000e+02 4.000000e+02 <br> 12 11 13 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br>
4 13 11 1 1.210000e+02 4.000000e+02 1.210000e+02 4.000000e+02 <br> 4 13 14 1 1.210000e+02 4.000000e+02 1.210000e+02 4.000000e+02 <br> 11 13 14 1 1.180000e+02 4.000000e+02 1.180000e+02 4.000000e+02 <br>
13 14 15 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 13 14 16 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 15 14 16 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br>
2 16 14 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 2 16 17 1 1.210000e+02 4.000000e+02 1.210000e+02 4.000000e+02 <br> 14 16 17 1 1.190000e+02 4.000000e+02 1.190000e+02 4.000000e+02 <br>
16 17 18 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 16 17 19 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 18 17 19 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br>
17 19 20 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 17 19 21 1 1.190000e+02 4.000000e+02 1.190000e+02 4.000000e+02 <br> 20 19 21 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br>
1 21 19 1 1.210000e+02 4.000000e+02 1.210000e+02 4.000000e+02 <br> 1 21 22 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 19 21 22 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br>
21 22 23 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 21 22 24 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 23 22 24 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br>
22 24 25 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 22 24 26 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 25 24 26 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br>
24 26 27 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 24 26 28 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 27 26 28 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br>
1 28 26 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 1 28 29 1 1.210000e+02 4.000000e+02 1.210000e+02 4.000000e+02 <br> 26 28 29 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br>
28 29 30 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 28 29 31 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br> 30 29 31 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02 <br>
3 31 29 1 1.220000e+02 4.000000e+02 1.220000e+02 4.000000e+02 <br> 3 31 32 1 1.190000e+02 4.000000e+02 1.190000e+02 4.000000e+02 <br> 29 31 32 1 1.190000e+02 4.000000e+02 1.190000e+02 4.000000e+02 <br>
<br>[ dihedrals ]<br>; ai aj ak al funct c0 c1 c2 c3<br> 1 2 21 28 1 1.800000e+02 5.000000e+00 1.800000e+02 5.000000e+00 <br> 2 1 3 16 1 1.800000e+02 5.000000e+00 1.800000e+02 5.000000e+00 <br>
3 2 4 31 1 1.800000e+02 5.000000e+00 1.800000e+02 5.000000e+00 <br> 4 3 5 13 1 1.800000e+02 5.000000e+00 1.800000e+02 5.000000e+00 <br> 5 4 6 7 1 1.800000e+02 5.000000e+00 1.800000e+02 5.000000e+00 <br>
7 5 8 9 1 1.800000e+02 5.000000e+00 1.800000e+02 5.000000e+00 <br> 9 7 10 11 1 1.800000e+02 5.000000e+00 1.800000e+02 5.000000e+00 <br> 11 9 12 13 1 1.800000e+02 5.000000e+00 1.800000e+02 5.000000e+00 <br>
13 4 11 14 1 1.800000e+02 5.000000e+00 1.800000e+02 5.000000e+00 <br> 14 13 15 16 1 1.800000e+02 5.000000e+00 1.800000e+02 5.000000e+00 <br> 16 2 14 17 1 1.800000e+02 5.000000e+00 1.800000e+02 5.000000e+00 <br>
17 16 18 19 1 1.800000e+02 5.000000e+00 1.800000e+02 5.000000e+00 <br> 19 17 20 21 1 1.800000e+02 5.000000e+00 1.800000e+02 5.000000e+00 <br> 21 1 19 22 1 1.800000e+02 5.000000e+00 1.800000e+02 5.000000e+00 <br>
22 21 23 24 1 1.800000e+02 5.000000e+00 1.800000e+02 5.000000e+00 <br> 24 22 25 26 1 1.800000e+02 5.000000e+00 1.800000e+02 5.000000e+00 <br> 26 24 27 28 1 1.800000e+02 5.000000e+00 1.800000e+02 5.000000e+00 <br>
28 1 26 29 1 1.800000e+02 5.000000e+00 1.800000e+02 5.000000e+00 <br> 29 28 30 31 1 1.800000e+02 5.000000e+00 1.800000e+02 5.000000e+00 <br> 31 3 29 32 1 1.800000e+02 5.000000e+00 1.800000e+02 5.000000e+00 <br>
<br><br><br><div class="gmail_quote">On Wed, Dec 22, 2010 at 7:36 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div><div></div><div class="h5"><br>
<br>
Sergio Manzetti wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
<br>
<br>
I am trying to grompp a molecule, but get the same error again:<br>
<br>
Program grompp, VERSION 4.5.1<br>
Source code file: topio.c, line: 654<br>
<br>
Fatal error:<br>
Syntax error - File bzp.itp, line 1<br>
Last line read:<br>
'[ moleculetype ]'<br>
Invalid order for directive moleculetype<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
<br>
<br>
Can any help?<br>
<br>
</blockquote>
<br></div></div>
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.<br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br><font color="#888888">
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