<div>Hi Justin,</div>
<div>Ok.Thanks for comments and advice, I appreciate.../Jamie<br><br></div>
<div class="gmail_quote">On Mon, Aug 10, 2009 at 3:06 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">Dear Vitaly and all,<br>I did copy my top file to a itp file and now for doing a md simulation I need a box of water and so I was thinking to make a .gro file and use editconf after that. But I did not know how, so I used the procedure by Christopher Stiles (I used editconf to make a gro file from pdb and I did not use my itp according to the procedure....) the gro file doesn't contain velocities. Now when I run the grompp command, I got this Fatal <br>
</blockquote><br></div>The .gro file will not contain velocities until you have run dynamics.
<div class="im"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">error:<br>Group BAL not found in indexfile....<br></blockquote><br></div>Then you have specified a molecule type that is not encompassed by your #included .itp files, or you have specified some special group in your .mdp file that doesn't exist without using a special index group.
<div class="im"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">my questions are<br>1) when I have my itp file and only I need a gro file (with velocities) how can I make it??<br>
</blockquote><br></div>I don't understand this question.
<div class="im"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">2) with Christopher Stiles method, why I got that fatal error and how I can solve it to run a correct md simulation??<br>
</blockquote><br></div>See above. Without seeing the topology and .mdp file, it is hard to provide any more useful advice.<br><br>I would seriously recommend running some simple tutorials on proteins (even if you don't care about proteins - these systems are very robust) to get a feel for procedures in Gromacs, how velocities are generated, how to use index files (if necessary), etc.<br>
<br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im">Many Thanks in advance/Jamie<br><br></div>
<div>
<div></div>
<div class="h5">On Mon, Aug 10, 2009 at 10:45 AM, Vitaly V. Chaban <<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 best solution is to copy all the sections ([atoms], [bonds], etc)<br> corresponding to each molecule into a separate file and then use<br> "include" statement like in C language to attach these .itp files to<br>
.top file.<br><br> So you will have only the numbers of the each kind of molecules in<br> your .top file. These manipulations are made only in the sake of<br> future comfort. Below is an example how I do it.<br><br>
Best,<br> Vitaly<br><br> ===============topology file==============<br> #include "vvc.itp"<br> #include "15x15x50.itp"<br> #include "20x20x50.itp"<br> #include "25x25x50.itp"<br>
<br><br> [ system ]<br> MWCNT with LIBF4 solution<br><br><br> [ molecules ]<br> 15x15x50 1<br> 20x20x50 1<br> 25x25x50 1<br> LI+ 7<br> BF4 7<br>
Methanol 254<br><br><br> On Mon, Aug 10, 2009 at 4:38 PM, Jamie Seyed<<a href="mailto:jamie.seyed@gmail.com" target="_blank">jamie.seyed@gmail.com</a><br></div></div>
<div class="im"> <mailto:<a href="mailto:jamie.seyed@gmail.com" target="_blank">jamie.seyed@gmail.com</a>>> wrote:<br> > Dear Vitaly,<br> > Thanks for your reply. Justin helped me about that and I could<br>
get the<br> > topology by x2top. In your last email you said after that I can<br> export it to<br> > the .itp right? Would you please explain more about that, I mean<br> for example<br> > should I change it manually to be look like a itp file or is that<br>
something<br> > else?? I appreciate your help...<br> > Thanks a lot/Jamie<br> ><br> > On Mon, Aug 10, 2009 at 2:18 AM, 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> >> Jamie,<br> >><br> >> What error messages do they provide? What force fields do you use?<br> >> There were many rumors about these utilities here in the list<br>
but they<br> >> seem to be workable in most cases.<br> >><br> >> Vitaly<br> >><br> >> On Mon, Aug 10, 2009 at 1:39 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>
>> > Actually it doe's not work. I tried but I got error messages<br> for both<br> >> > cases.<br> >> > Actually the structure is big and contains a c60 part. Do you<br> have any<br>
>> > advice? I could not find in the topology part of archive...<br> >> > Thanks/Jamie<br> >> ><br> >> ><br> >> > On Sun, Aug 9, 2009 at 2:54 AM, 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>
<div></div>
<div class="h5"><br> >> > wrote:<br> >> >><br> >> >> Hi,<br> >> >><br> >> >> Did you try pdb2gmx, x2top to make .top and then export to .itp?<br> >> >> Sometimes also it appears easier to make the topology by hand<br>
if your<br> >> >> structure is not big. Please see the topologies for some<br> molecules in<br> >> >> the gromacs archive to use them as an example.<br> >> >><br> >> >> Vitaly<br>
>> >><br> >> >> ><br> >> >> > Dear gmx users,<br> >> >> > I need some help for generating a itp file for my molecular<br> >> >> > structure. I<br>
>> >> > am<br> >> >> > using molden and now I have the xyz and pdb files. I read<br> through<br> >> >> > mailing<br> >> >> > list but seems I should provide itp myself. But I don't<br>
know the<br> >> >> > right<br> >> >> > way<br> >> >> > to do that. Is it using molden and find one-by-one bond<br> sand angles<br> >> >> > and<br>
>> >> > dihedrals... . If I have already the itp file for a part of<br> molecule<br> >> >> > is<br> >> >> > it<br> >> >> > only to add the information of new atoms to the old itp<br>
file?? I will<br> >> >> > really<br> >> >> > appreciate it if someone gives me better ideas and more related<br> >> >> > information<br> >> >> > to make my itp file.<br>
>> >> ><br> >> >> > Many Thanks in Advance,<br> >> >> > Jamie<br> >> >> > -------------- next part --------------<br> >> >> > An HTML attachment was scrubbed...<br>
>> >> > URL:<br> >> >> ><br> >> >> ><br> <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20090808/aaef0139/attachment-0001.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20090808/aaef0139/attachment-0001.html</a><br>
>> >> _______________________________________________<br> >> >> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div></div> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>
<div class="im"><br> >> >> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br> >> >> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
>> >> posting!<br> >> >> Please don't post (un)subscribe requests to the list. Use the<br> >> >> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
</div> <mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.
<div class="im"><br> >> >> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br> >> ><br> >> ><br>
>><br> >><br> >><br> >> --<br> >> Vitaly V. Chaban, Ph.D. (ABD)<br> >> School of Chemistry<br> >> V.N. Karazin Kharkiv National University<br> >> Svoboda sq.,4, Kharkiv 61077, Ukraine<br>
>> email: <a href="mailto:chaban@univer.kharkov.ua" target="_blank">chaban@univer.kharkov.ua</a><br></div> <mailto:<a href="mailto:chaban@univer.kharkov.ua" target="_blank">chaban@univer.kharkov.ua</a>>,<a href="mailto:vvchaban@gmail.com" target="_blank">vvchaban@gmail.com</a><br>
<mailto:<a href="mailto:vvchaban@gmail.com" target="_blank">vvchaban@gmail.com</a>>
<div class="im"><br> >> skype: vvchaban, cell.: +38-097-8259698<br> >> <a href="http://www-rmn.univer.kharkov.ua/chaban.html" target="_blank">http://www-rmn.univer.kharkov.ua/chaban.html</a><br> >> ===================================<br>
>> !!! Looking for a postdoctoral position !!!<br> >> ===================================<br> ><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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Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></div></blockquote><br>-- <br>
<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></div>
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