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 <vvcha...@gmail.com
<mailto:vvcha...@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.se...@gmail.com
<mailto:jamie.se...@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
<vvcha...@gmail.com <mailto:vvcha...@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.se...@gmail.com <mailto:jamie.se...@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
<vvcha...@gmail.com <mailto:vvcha...@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: cha...@univer.kharkov.ua
<mailto:cha...@univer.kharkov.ua>,vvcha...@gmail.com
<mailto:vvcha...@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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