[gmx-users] Re: itp file
Jamie Seyed
jamie.seyed at gmail.com
Mon Aug 10 21:23:57 CEST 2009
Hi Justin,
Ok.Thanks for comments and advice, I appreciate.../Jamie
On Mon, Aug 10, 2009 at 3:06 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
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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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