<div>Dear all,</div>
<div>I have a topology contains line as below. I do not understand what is wrong with it that I get an error </div>
<div>-----------<br> Program grompp, Version 4.0.5<br> Source Code file: topio.c, line: 415<br> Fatal error:<br> Syntax error-File ffoplsaa.itp, line 18<br> last line read:<br> '[defaults]'<br> Invalid order for directive defaults<br>
--------------<br>according to the page <a href="http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file">http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file</a></div>
<div>I do not have twice default section... SO I do not know exactly which files I should check... It says topology and ff. Topology that I am using in grompp is as below and the ffoplsaa.itp has only one default section...</div>
<div>Would you please help me to solve the problem.</div>
<div>
<div>topol.top: -------------</div>
<div>#include "ffoplsaa.itp"</div>
<div>#include "spce.itp"<br>#include "molecule.itp"<br>[system]</div>
<div>fullerene in water</div>
<div>[molecules]</div>
<div>molecule 1</div>
<div>SOL 1000</div>
<div>--------------------</div></div>
<div>Many Thanks in Advance and I appreciate your help/Jamie</div>
<div><br> </div>
<div class="gmail_quote">On Mon, Aug 10, 2009 at 5:46 PM, Jamie Seyed <span dir="ltr"><<a href="mailto:jamie.seyed@gmail.com">jamie.seyed@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div>Dear Vitaly,</div>
<div>topol.top: -------------</div>
<div>#include "ffoplsaa.itp"</div>
<div>#include "spce.itp"<br>#include "c80ch3.itp"<br>[system]</div>
<div>fullerene in water</div>
<div>[molecules]</div>
<div>C80CH3 1</div>
<div>SOL 1000</div>
<div>--------------------</div>
<div>my command is:</div>
<div>grompp -f md.mdp -c f.gro -p topol.top -o pr.tpr -maxwarn 10</div>
<div> </div>
<div>Thank you for helping me out to solve the problem/ Regards/Jamie</div>
<div>
<div></div>
<div class="h5">
<div> </div>
<div> </div>
<div class="gmail_quote">On Mon, Aug 10, 2009 at 5:39 PM, Vitaly V. Chaban <span dir="ltr"><<a href="mailto:vvchaban@gmail.com" target="_blank">vvchaban@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Jamie,<br><br>The idea is the same. Some directive is not at its place. I cannot say<br>which is exactly because I don't see all the picture with your<br>
topology file (+included files). Write the sequence of directives as<br>they go in .top (+included .itp) and then we will see what sections<br>must be shifted or maybe just swapped.<br><font color="#888888"><br>Vitaly<br>
</font>
<div><br>On Tue, Aug 11, 2009 at 12:34 AM, Jamie Seyed<<a href="mailto:jamie.seyed@gmail.com" target="_blank">jamie.seyed@gmail.com</a>> wrote:<br>> Hi Vitaly,<br></div>
<div>
<div></div>
<div>> When I add it back, I got the old error<br>> -----------<br>> Program grompp, Version 4.0.5<br>> Source Code file: topio.c, line: 415<br>> Fatal error:<br>> Syntax error-File ffoplsaa.itp, line 18<br>
> last line read:<br>> '[defaults]'<br>> Invalid order for directive defaults<br>> -----------<br>> Now do you have any idea??? I appreciate your help/Jamie<br>><br>> On Mon, Aug 10, 2009 at 5:22 PM, Jamie Seyed <<a href="mailto:jamie.seyed@gmail.com" target="_blank">jamie.seyed@gmail.com</a>> wrote:<br>
>><br>>> Hi Vitaly,<br>>> I did it because I read from<br>>> <a href="http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file" target="_blank">http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file</a><br>
>> that says:<br>>> "One solution is to simply comment out (or delete) the lines of code out<br>>> in the file where it is included for the second time i.e., ..". So if it is<br>>> the case I am going to undo it to see what happens... I will let you know.<br>
>> Thanks/Jamie<br>>> On Mon, Aug 10, 2009 at 5:05 PM, Vitaly V. Chaban <<a href="mailto:vvchaban@gmail.com" target="_blank">vvchaban@gmail.com</a>><br>>> wrote:<br>>>><br>>>> Why did you comment out [defaults] in ffoplsaa.itp? The general idea<br>
>>> is that the sections in the resulting topology file (after including<br>>>> #include's) must be placed in the strict order.<br></div></div></blockquote></div><br></div></div></blockquote></div><br>