[gmx-users] Re: itp file

Mon Aug 10 20:53:04 CEST 2009

Dear Vitaly and all,
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:
Group BAL not found in indexfile....
my questions are
1) when I have my itp file and only I need a gro file (with velocities) how
can I make it??
2) with Christopher Stiles method, why I got that fatal error and how I can
solve it to run a correct md simulation??
Many Thanks in advance/Jamie

On Mon, Aug 10, 2009 at 10:45 AM, Vitaly V. Chaban <vvchaban at gmail.com>wrote:

> Jamie,
>
> The best solution is to copy all the sections ([atoms], [bonds], etc)
> corresponding to each molecule into a separate file and then use
> "include" statement like in C language to attach these .itp files to
> .top file.
>
> So you will have only the numbers of the each kind of molecules in
> your .top file. These manipulations are made only in the sake of
> future comfort. Below is an example how I do it.
>
> Best,
>   Vitaly
>
> ===============topology  file==============
> #include "vvc.itp"
> #include "15x15x50.itp"
> #include "20x20x50.itp"
> #include "25x25x50.itp"
>
>
> [ system ]
> MWCNT with LIBF4 solution
>
>
> [ molecules ]
> 15x15x50              1
> 20x20x50              1
> 25x25x50              1
> LI+                          7
> BF4                        7
> Methanol           254
>
>
> On Mon, Aug 10, 2009 at 4:38 PM, Jamie Seyed<jamie.seyed at gmail.com> wrote:
> > Dear Vitaly,
> > Thanks for your reply. Justin helped me about that and I could get the
> > topology by x2top. In your last email you said after that I can export it
> to
> > the .itp right? Would you please explain more about that, I mean for
> example
> > should I change it manually to be look like a itp file or is that
> something
> > else?? I appreciate your help...
> > Thanks a lot/Jamie
> >
> > On Mon, Aug 10, 2009 at 2:18 AM, Vitaly V. Chaban <vvchaban at gmail.com>
> > wrote:
> >>
> >> Jamie,
> >>
> >> What error messages do they provide? What force fields do you use?
> >> There were many rumors about these utilities here in the list but they
> >> seem to be workable in most cases.
> >>
> >> Vitaly
> >>
> >> On Mon, Aug 10, 2009 at 1:39 AM, Jamie Seyed<jamie.seyed at gmail.com>
> wrote:
> >> > Hi Vitaly,
> >> > Actually it doe's not work. I tried but I got error messages for both
> >> > cases.
> >> > Actually the structure is big and contains a c60 part. Do you have any
> >> > advice? I could not find in the topology part of archive...
> >> > Thanks/Jamie
> >> >
> >> >
> >> > On Sun, Aug 9, 2009 at 2:54 AM, Vitaly V. Chaban <vvchaban at gmail.com>
> >> > wrote:
> >> >>
> >> >> Hi,
> >> >>
> >> >> Did you try pdb2gmx, x2top to make .top and then export to .itp?
> >> >> Sometimes also it appears easier to make the topology by hand if your
> >> >> structure is not big. Please see the topologies for some molecules in
> >> >> the gromacs archive to use them as an example.
> >> >>
> >> >> Vitaly
> >> >>
> >> >> >
> >> >> > Dear gmx users,
> >> >> > I need some help for generating a itp file for my molecular
> >> >> > structure. I
> >> >> > am
> >> >> > using molden and now I have the xyz and pdb files. I read through
> >> >> > mailing
> >> >> > list but seems I should provide itp myself. But I don't know the
> >> >> > right
> >> >> > way
> >> >> > to do that. Is it using molden and find one-by-one bond sand angles
> >> >> > and
> >> >> > dihedrals... . If I have already the itp file for a part of
> molecule
> >> >> > is
> >> >> > it
> >> >> > only to add the information of new atoms to the old itp file?? I
> will
> >> >> > really
> >> >> > appreciate it if someone gives me better ideas and more related
> >> >> > information
> >> >> > to make my itp file.
> >> >> >
> >> >> > Many Thanks in Advance,
> >> >> > Jamie
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> >>
> >>
> >>
> >> --
> >> Vitaly V. Chaban, Ph.D. (ABD)
> >> School of Chemistry
> >> V.N. Karazin Kharkiv National University
> >> Svoboda sq.,4, Kharkiv 61077, Ukraine
> >> email: chaban at univer.kharkov.ua,vvchaban at gmail.com
> >> skype: vvchaban, cell.: +38-097-8259698
> >> http://www-rmn.univer.kharkov.ua/chaban.html
> >> ===================================
> >> !!! Looking for a postdoctoral position !!!
> >> ===================================
> >
> >
>
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