<div>Dear Vitaly and all,</div>
<div>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 error:</div>
<div>Group BAL not found in indexfile....</div>
<div>my questions are</div>
<div>1) when I have my itp file and only I need a gro file (with velocities) how can I make it??</div>
<div>2) with Christopher Stiles method, why I got that fatal error and how I can solve it to run a correct md simulation??</div>
<div>Many Thanks in advance/Jamie<br><br></div>
<div class="gmail_quote">On Mon, Aug 10, 2009 at 10:45 AM, Vitaly V. Chaban <span dir="ltr"><<a href="mailto:vvchaban@gmail.com">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 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>
<div>
<div></div>
<div class="h5"><br><br>On Mon, Aug 10, 2009 at 4:38 PM, Jamie Seyed<<a href="mailto:jamie.seyed@gmail.com">jamie.seyed@gmail.com</a>> wrote:<br>> Dear Vitaly,<br>> Thanks for your reply. Justin helped me about that and I could get the<br>
> topology by x2top. In your last email you said after that I can export it to<br>> the .itp right? Would you please explain more about that, I mean for example<br>> should I change it manually to be look like a itp file or is that 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 <<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a>><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 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 Seyed<<a href="mailto:jamie.seyed@gmail.com">jamie.seyed@gmail.com</a>> wrote:<br>>> > Hi Vitaly,<br>>> > Actually it doe's not work. I tried but I got error messages for both<br>
>> > cases.<br>>> > Actually the structure is big and contains a c60 part. Do you 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 <<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a>><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 if your<br>>> >> structure is not big. Please see the topologies for some 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 through<br>>> >> > mailing<br>>> >> > list but seems I should provide itp myself. But I don't know the<br>
>> >> > right<br>>> >> > way<br>>> >> > to do that. Is it using molden and find one-by-one bond sand angles<br>>> >> > and<br>>> >> > dihedrals... . If I have already the itp file for a part of molecule<br>
>> >> > is<br>>> >> > it<br>>> >> > only to add the information of new atoms to the old itp 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>>> >> > <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">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>
>> >> 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">gmx-users-request@gromacs.org</a>.<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">chaban@univer.kharkov.ua</a>,<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a><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></div></div></blockquote></div><br>