[gmx-users] Re: itp file
Vitaly V. Chaban
vvchaban at gmail.com
Mon Aug 10 22:29:51 CEST 2009
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 --------------
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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 !!!
===================================
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