[gmx-users] Re: itp file

[Vitaly V. Chaban]

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 !!!
>> ===================================
>
>