[gmx-users] Re: itp file
Justin A. Lemkul
jalemkul at vt.edu
Mon Aug 10 21:06:02 CEST 2009
Jamie Seyed wrote:
> 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
The .gro file will not contain velocities until you have run dynamics.
> error:
> Group BAL not found in indexfile....
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.
> my questions are
> 1) when I have my itp file and only I need a gro file (with velocities)
> how can I make it??
I don't understand this question.
> 2) with Christopher Stiles method, why I got that fatal error and how I
> can solve it to run a correct md simulation??
See above. Without seeing the topology and .mdp file, it is hard to provide any
more useful advice.
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.
-Justin
> Many Thanks in advance/Jamie
>
> On Mon, Aug 10, 2009 at 10:45 AM, Vitaly V. Chaban <vvchaban at gmail.com
> <mailto: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
> <mailto: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 <mailto: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 <mailto: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 <mailto: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
> >> >> > -------------- next part --------------
> >> >> > An HTML attachment was scrubbed...
> >> >> > URL:
> >> >> >
> >> >> >
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20090808/aaef0139/attachment-0001.html
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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
> <mailto:chaban at univer.kharkov.ua>,vvchaban at gmail.com
> <mailto: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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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