[gmx-users] Re: itp file
Vitaly V. Chaban
vvchaban at gmail.com
Mon Aug 10 23:05:52 CEST 2009
Why did you comment out [defaults] in ffoplsaa.itp? The general idea
is that the sections in the resulting topology file (after including
#include's) must be placed in the strict order.
On Mon, Aug 10, 2009 at 11:50 PM, Jamie Seyed<jamie.seyed at gmail.com> wrote:
> Hi Vitaly,
> Thanks for your good comments. Yes I deleted that and I run the program but
> finally I found a line that said 26 inconsistent shifts....
> So I tried to do everything again properly. Now I faced with several
> problems and to get rid of them:
> I put ff*.itp in the top line of topol.top, I commented out the line
> [defaults] in ffoplsaa.itp
> but now I have a new error that
> -----------------------------
> Fatal error: syntax eror -File ffoplsaanb.itp, line 1
> last line read:
> '[atomtype]'
> Invalid order for directive atomtype
> ----------------------------
> I did not mixed the ff and I put ff.itp on the top of my topology file...
> would you please let me know what is causing the problem?? I appreciate your
> help.../Jamie
>
> On Mon, Aug 10, 2009 at 4:29 PM, Vitaly V. Chaban <vvchaban at gmail.com>
> wrote:
>>
>> Dear Jamie,
>>
>> > 1) when I have my itp file and only I need a gro file (with velocities)
>> > how
>> > can I make it??
>> .gro can be made from .pdb with editconf. Also you will find useful
>> genbox and genconf for the related tasks. The velocities are not
>> needed to start MD run. They can be assigned automatically by mdrun
>> with "gen_vel" keyword in grompp.mdp.
>>
>> > 2) with Christopher Stiles method, why I got that fatal error and how I
>> > can
>> > solve it to run a correct md simulation??
>> What is the group BAL in your system? I guess you mentioned it in the
>> .mdp file, so the program looks for it and doesn't find anywhere.
>> Either delete it from .mdp or provide an information which atoms this
>> group contains (see "-n index.ndx").
>>
>> Good luck,
>> Vitaly
>>
>> On Mon, Aug 10, 2009 at 9:53 PM, Jamie Seyed<jamie.seyed at gmail.com> 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 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
>> >> >> >> > -------------- 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,vvchaban at gmail.com
>> >> >> skype: vvchaban, cell.: +38-097-8259698
>> >> >> http://www-rmn.univer.kharkov.ua/chaban.html
>> >> >> ===================================
>> >> >> !!! Looking for a postdoctoral position !!!
>> >> >> ===================================
>> >> >
>> >> >
>> >
>> >
>>
>>
>>
>> --
>> 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 !!!
>> ===================================
>
>
--
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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