<div>Hi Justin,</div>
<div>Oh yes. I had a line that include ff again and I deleted that (is that ok)? now I got a new error related to "number of coordinates in coordinate file does not match topology..." I should fix this one now!! Thanks a lot/Jamie<br>
<br></div>
<div class="gmail_quote">On Mon, Aug 10, 2009 at 8:10 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="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br>Can you post the contents of molecule.itp? The first #include for the force field is likely not the problem; you've probably #included it again in molecule.itp.<br>
<br>-Justin<br><br>Jamie Seyed wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im">Dear all,<br>I have a topology contains line as below. I do not understand what is wrong with it that I get an 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>according to the page <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>
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...<br>
Would you please help me to solve the problem.<br>topol.top: -------------<br>#include "ffoplsaa.itp"<br>#include "spce.itp"<br>#include "molecule.itp"<br>[system]<br>fullerene in water<br>[molecules]<br>
molecule 1<br>SOL 1000<br>--------------------<br>Many Thanks in Advance and I appreciate your help/Jamie<br><br></div>
<div class="im"> On Mon, Aug 10, 2009 at 5:46 PM, Jamie Seyed <<a href="mailto:jamie.seyed@gmail.com" target="_blank">jamie.seyed@gmail.com</a> <mailto:<a href="mailto:jamie.seyed@gmail.com" target="_blank">jamie.seyed@gmail.com</a>>> wrote:<br>
<br> Dear Vitaly,<br> topol.top: -------------<br> #include "ffoplsaa.itp"<br> #include "spce.itp"<br> #include "c80ch3.itp"<br> [system]<br> fullerene in water<br> [molecules]<br>
C80CH3 1<br> SOL 1000<br> --------------------<br> my command is:<br> grompp -f md.mdp -c f.gro -p topol.top -o pr.tpr -maxwarn 10<br> Thank you for helping me out to solve the problem/ Regards/Jamie<br>
On Mon, Aug 10, 2009 at 5:39 PM, Vitaly V. Chaban<br></div>
<div class="im"> <<a href="mailto:vvchaban@gmail.com" target="_blank">vvchaban@gmail.com</a> <mailto:<a href="mailto:vvchaban@gmail.com" target="_blank">vvchaban@gmail.com</a>>> wrote:<br><br> Jamie,<br>
<br> The idea is the same. Some directive is not at its place. I<br> 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><br> Vitaly<br><br> On Tue, Aug 11, 2009 at 12:34 AM, Jamie<br></div>
<div class="im"> Seyed<<a href="mailto:jamie.seyed@gmail.com" target="_blank">jamie.seyed@gmail.com</a> <mailto:<a href="mailto:jamie.seyed@gmail.com" target="_blank">jamie.seyed@gmail.com</a>>> wrote:<br>
> Hi Vitaly,<br> > 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<br></div>
<div class="im"> <<a href="mailto:jamie.seyed@gmail.com" target="_blank">jamie.seyed@gmail.com</a> <mailto:<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> >><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<br> of code out<br> >> in the file where it is included for the second time i.e.,<br> ..". So if it is<br>
>> the case I am going to undo it to see what happens... I will<br> let you know.<br> >> Thanks/Jamie<br> >> On Mon, Aug 10, 2009 at 5:05 PM, Vitaly V. Chaban<br></div> <<a href="mailto:vvchaban@gmail.com" target="_blank">vvchaban@gmail.com</a> <mailto:<a href="mailto:vvchaban@gmail.com" target="_blank">vvchaban@gmail.com</a>>>
<div class="im"><br> >> wrote:<br> >>><br> >>> Why did you comment out [defaults] in ffoplsaa.itp? The<br> general idea<br> >>> is that the sections in the resulting topology file (after<br>
including<br> >>> #include's) must be placed in the strict order.<br><br><br><br><br></div>------------------------------------------------------------------------
<div class="im"><br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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<div class="im">========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<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>_______________________________________________<br>
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