<div>Hi Justin,</div>
<div>Thanks again... . Actully I have a question: I have 1836 atoms (572 water and 1 molecule with 120 atoms). In top of my file.gro I have 1836 and in topology in [molecules] I have c60ch3 1; and SOL 572 which means the same as above. So how I should change it to get rid of error...??/ Thank you in advance.../Jamie<br>
</div>
<div class="gmail_quote">On Mon, Aug 10, 2009 at 8:20 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">
<div class="im"><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">Hi Justin,<br>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 <br>
</blockquote><br></div>That's more than OK, that's correct. As Mark pointed out, there should only ever be one invocation of [ defaults ] in a topology.
<div class="im"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">coordinate file does not match topology..." I should fix this one now!! <br></blockquote><br></div>Simple one to fix. Figure out where the duplicate or missing molecules are within the topology. I'm guessing your molecule.itp was really a molecule.top, complete with [ defaults ], [ system ], and [ molecules ] directive, right? None of these should be present in an .itp file, only a .top.<br>
<br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Thanks a lot/Jamie
<div>
<div></div>
<div class="h5"><br><br>On Mon, Aug 10, 2009 at 8:10 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br><br> Can you post the contents of molecule.itp? The first #include for<br> the force field is likely not the problem; you've probably #included<br> it again in molecule.itp.<br><br> -Justin<br><br> Jamie Seyed wrote:<br>
<br> Dear all,<br> I have a topology contains line as below. I do not understand<br> 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<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> I do not have twice default section... SO I do not know exactly<br>
which files I should check... It says topology and ff. Topology<br> that I am using in grompp is as below and the ffoplsaa.itp has<br> 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> On Mon, Aug 10, 2009 at 5:46 PM, Jamie Seyed<br> <<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>><br>
</div></div> <mailto:<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>>>>
<div class="im"><br> 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/<br> Regards/Jamie<br> On Mon, Aug 10, 2009 at 5:39 PM, Vitaly V. Chaban<br> <<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>><br>
</div>
<div class="im"> <mailto:<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<br> your<br>
topology file (+included files). Write the sequence of<br> directives as<br> they go in .top (+included .itp) and then we will see<br> 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> Seyed<<a href="mailto:jamie.seyed@gmail.com" target="_blank">jamie.seyed@gmail.com</a><br></div> <mailto:<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>
<div class="im"><br> <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> <<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>><br>
</div> <mailto:<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>>>>
<div class="im"><br> 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)<br> the lines<br> of code out<br> >> in the file where it is included for the second time<br>
i.e.,<br> ..". So if it is<br> >> the case I am going to undo it to see what happens...<br> I will<br> let you know.<br> >> Thanks/Jamie<br>
>> On Mon, Aug 10, 2009 at 5:05 PM, Vitaly V. Chaban<br> <<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>><br>
</div> <mailto:<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><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<br>
(after<br> including<br> >>> #include's) must be placed in the strict order.<br><br><br><br><br> ------------------------------------------------------------------------<br>
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<div class="h5"><br>-- <br>========================================<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>
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