Thank you so much for your quick reply!<div><br></div><div>Below please find my topology file: </div><div><br></div><div><br></div><div><div>; Include forcefield parameters</div><div>#include "hautklein.ff/forcefield.itp"</div>
<div><br></div><div>[ moleculetype ]</div><div>; Name nrexcl</div><div>Protein_chain_1 3</div><div><br></div><div>[ atoms ]</div><div>; nr type resnr residue atom cgnr charge mass typeB chargeB massB</div>
<div>; residue 0 ALK rtp ALK q 0.0</div><div> 1 CH3 0 ALK CH3 1 0 15.035 ; qtot 0</div><div> 2 CH2 0 ALK CH2A 2 0 14.027 ; qtot 0</div>
<div> 3 CH2 0 ALK CH2B 3 0 14.027 ; qtot 0</div><div> 4 CH2 0 ALK CH2C 4 0 14.027 ; qtot 0</div><div> 5 CH2 0 ALK CH2D 5 0 14.027 ; qtot 0</div>
<div> 6 CH2 0 ALK CH2E 6 0 14.027 ; qtot 0</div><div> 7 CH2 0 ALK CH2F 7 0 14.027 ; qtot 0</div><div> 8 CH2 0 ALK CH2G 8 0 14.027 ; qtot 0</div>
<div> 9 CH2 0 ALK CH2H 9 0 14.027 ; qtot 0</div><div> 10 CH2 0 ALK CH2I 10 0 14.027 ; qtot 0</div><div> 11 CH2 0 ALK CH2J 11 0 14.027 ; qtot 0</div>
<div> 12 CH2 0 ALK CH2K 12 0 14.027 ; qtot 0</div><div> 13 S 0 ALK S 13 0 32.06 ; qtot 0</div><div><br></div><div>[ bonds ]</div><div>; ai aj funct c0 c1 c2 c3</div>
<div> 1 2 1</div><div> 2 3 1</div><div> 3 4 1</div><div> 4 5 1</div><div> 5 6 1</div><div> 6 7 1</div><div> 7 8 1</div><div> 8 9 1</div>
<div> 9 10 1</div><div> 10 11 1</div><div> 11 12 1</div><div> 12 13 1</div><div><br></div><div>[ pairs ]</div><div>; ai aj funct c0 c1 c2 c3</div>
<div> 1 4 1</div><div> 2 5 1</div><div> 3 6 1</div><div> 4 7 1</div><div> 5 8 1</div><div> 6 9 1</div><div> 7 10 1</div><div> 8 11 1</div>
<div> 9 12 1</div><div> 10 13 1</div><div><br></div><div>[ angles ]</div><div>; ai aj ak funct c0 c1 c2 c3</div><div> 1 2 3 1</div><div>
2 3 4 1</div><div> 3 4 5 1</div><div> 4 5 6 1</div><div> 5 6 7 1</div><div> 6 7 8 1</div><div> 7 8 9 1</div><div> 8 9 10 1</div>
<div> 9 10 11 1</div><div> 10 11 12 1</div><div> 11 12 13 1</div><div><br></div><div>[ dihedrals ]</div><div>; ai aj ak al funct c0 c1 c2 c3 c4 c5</div>
<div> 1 2 3 4 3</div><div> 2 3 4 5 3</div><div> 3 4 5 6 3</div><div> 4 5 6 7 3</div><div> 5 6 7 8 3</div><div> 6 7 8 9 3</div>
<div> 7 8 9 10 3</div><div> 8 9 10 11 3</div><div> 9 10 11 12 3</div><div> 10 11 12 13 3</div><div><br></div><div>[ constraints ]</div><div>; i j funct b0</div>
<div> 1 2 1 0.0153</div><div> 2 3 1 0.0153</div><div> 3 4 1 0.0153</div><div> 4 5 1 0.0153</div><div> 5 6 1 0.0153</div><div> 6 7 1 0.0153</div>
<div> 7 8 1 0.0153</div><div> 8 9 1 0.0153</div><div> 9 10 1 0.0153</div><div> 10 11 1 0.0153</div><div> 11 12 1 0.0153</div><div> 12 13 1 0.0182</div>
<div><br></div><div>; Include Position restraint file</div><div>#ifdef POSRES</div><div>#include "posre.itp"</div><div>#endif</div><div><br></div><div>[ system ]</div><div>; Name</div><div>Protein</div><div><br>
</div><div>[ molecules ]</div><div>; Compound #mols</div><div>Protein_chain_1 1</div><div> </div><div>Does this help?</div><div><br></div><div>Thanks so much again,</div><div>Olivia </div>
<br><div class="gmail_quote">On Tue, Nov 1, 2011 at 5:49 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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
Olivia Waring wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gromacs users,<br>
<br>
First of all, many thanks to Justin for his assistance with my previous question.<br>
<br>
I have defined a new residue type in the oplsaa force field, changing the aminoacids.rtp file accordingly. pdb2gmx worked just fine; but when I try to preprocess, I get the following output: <br>
WARNING 1 [file ffbonded.itp, line 58]:<br>
Overriding Bond parameters.<br>
<br>
old: 0.1229 476976 0.1229 476976<br>
new: C O 1 0.13270 179075.2<br>
<br>
<br>
WARNING 2 [file ffbonded.itp, line 64]:<br>
Overriding Bond parameters.<br>
<br>
old: 0.1522 265266 0.1522 265266<br>
new: C CT 1 0.14950 265265.6<br>
<br>
<br>
WARNING 3 [file ffbonded.itp, line 67]:<br>
Overriding Bond parameters.<br>
<br>
old: 0.149 334720 0.149 334720<br>
new: CA C 1 0.14240 392459.2<br>
<br>
<br>
WARNING 4 [file ffbonded.itp, line 73]:<br>
Overriding Bond parameters.<br>
<br>
old: 0.1419 374050 0.1419 374050<br>
new: C CB 1 0.14240 392459.2<br>
<br>
</blockquote>
<br></div>
These four warnings suggest you're using values for bonded parameters that conflict with those present in the force field. If you have reason to do this, then there's no problem, per se. But be aware that you're using parameters the force field does not expect.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
------------------------------<u></u>-------------------------<br>
Program grompp, VERSION 4.5.4<br>
Source code file: topdirs.c, line: 76<br>
<br>
Fatal error:<br>
Invalid bond type 0<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/<u></u>Documentation/Errors</a><br>
<br>
<br>
The error is rather cryptic, and I'm having trouble tracking it down... I even went to the source code (topdirs.c), but I'm still not sure where exactly this "invalid bond type" is being defined. <br>
</blockquote>
<br></div>
This error suggests a more fundamental problem in your topology, but without seeing the topology, there's little more that can be said.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<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> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br><font color="#888888">
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</font></blockquote></div><br><br clear="all"><div><br></div>-- <br><div>Olivia Waring (王维娅)</div>
<div>Princeton University '12</div>
<div>AB Chemistry</div><br>
</div>