On Mon, Aug 10, 2009 at 8:36 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Jamie Seyed wrote:
Hi Justin,
Thanks again... . Actully I have a question: I have 1836 atoms
(572 water and 1 molecule with 120 atoms). In top of my file.gro
I have 1836 and in topology in [molecules] I have c60ch3 1; and
SOL 572 which means the same as above. So how I should change it
to get rid of error...??/
The above should be correct. However, you then have in your .top
you posted earlier:
[molecules]
molecule 1
SOL 1000
This section is probably the source of your problem. Again, as I
said before, there should only ever be one [ molecules ] section in
the .top file. Sounds like you've got two.
-Justin
Thank you in advance.../Jamie
On Mon, Aug 10, 2009 at 8:20 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Jamie Seyed wrote:
Hi Justin,
Oh yes. I had a line that include ff again and I deleted that
(is that ok)? now I got a new error related to "number of
coordinates in
That's more than OK, that's correct. As Mark pointed out, there
should only ever be one invocation of [ defaults ] in a topology.
coordinate file does not match topology..." I should fix this
one now!!
Simple one to fix. Figure out where the duplicate or missing
molecules are within the topology. I'm guessing your
molecule.itp
was really a molecule.top, complete with [ defaults ], [
system ],
and [ molecules ] directive, right? None of these should be
present
in an .itp file, only a .top.
-Justin
Thanks a lot/Jamie
On Mon, Aug 10, 2009 at 8:10 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> wrote:
Can you post the contents of molecule.itp? The first
#include for
the force field is likely not the problem; you've probably
#included
it again in molecule.itp.
-Justin
Jamie Seyed wrote:
Dear all,
I have a topology contains line as below. I do not
understand
what is wrong with it that I get an error
-----------
Program grompp, Version 4.0.5
Source Code file: topio.c, line: 415
Fatal error:
Syntax error-File ffoplsaa.itp, line 18
last line read:
'[defaults]'
Invalid order for directive defaults
--------------
according to the page
http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
I do not have twice default section... SO I do not
know
exactly
which files I should check... It says topology and ff.
Topology
that I am using in grompp is as below and the
ffoplsaa.itp has
only one default section...
Would you please help me to solve the problem.
topol.top: -------------
#include "ffoplsaa.itp"
#include "spce.itp"
#include "molecule.itp"
[system]
fullerene in water
[molecules]
molecule 1
SOL 1000
--------------------
Many Thanks in Advance and I appreciate your
help/Jamie
On Mon, Aug 10, 2009 at 5:46 PM, Jamie Seyed
<jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com> <mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>>
<mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com> <mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>>>
<mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>
<mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>> <mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>
<mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>>>>>
wrote:
Dear Vitaly,
topol.top: -------------
#include "ffoplsaa.itp"
#include "spce.itp"
#include "c80ch3.itp"
[system]
fullerene in water
[molecules]
C80CH3 1
SOL 1000
--------------------
my command is:
grompp -f md.mdp -c f.gro -p topol.top -o pr.tpr
-maxwarn 10
Thank you for helping me out to solve the
problem/
Regards/Jamie
On Mon, Aug 10, 2009 at 5:39 PM, Vitaly
V. Chaban
<vvcha...@gmail.com <mailto:vvcha...@gmail.com>
<mailto:vvcha...@gmail.com <mailto:vvcha...@gmail.com>>
<mailto:vvcha...@gmail.com <mailto:vvcha...@gmail.com>
<mailto:vvcha...@gmail.com <mailto:vvcha...@gmail.com>>>
<mailto:vvcha...@gmail.com
<mailto:vvcha...@gmail.com> <mailto:vvcha...@gmail.com
<mailto:vvcha...@gmail.com>>
<mailto:vvcha...@gmail.com <mailto:vvcha...@gmail.com>
<mailto:vvcha...@gmail.com <mailto:vvcha...@gmail.com>>>>> wrote:
Jamie,
The idea is the same. Some directive is not
at its
place. I
cannot say
which is exactly because I don't see all the
picture with
your
topology file (+included files). Write the
sequence of
directives as
they go in .top (+included .itp) and then
we will see
what sections
must be shifted or maybe just swapped.
Vitaly
On Tue, Aug 11, 2009 at 12:34 AM, Jamie
Seyed<jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>
<mailto:jamie.se...@gmail.com <mailto:jamie.se...@gmail.com>>
<mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>
<mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>>> <mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>
<mailto:jamie.se...@gmail.com <mailto:jamie.se...@gmail.com>>
<mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>
<mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>>>>> wrote:
> Hi Vitaly,
> When I add it back, I got the old error
> -----------
> Program grompp, Version 4.0.5
> Source Code file: topio.c, line: 415
> Fatal error:
> Syntax error-File ffoplsaa.itp, line 18
> last line read:
> '[defaults]'
> Invalid order for directive defaults
> -----------
> Now do you have any idea??? I appreciate
your
help/Jamie
>
> On Mon, Aug 10, 2009 at 5:22 PM, Jamie Seyed
<jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>
<mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>> <mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>
<mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>>>
<mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>
<mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>> <mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>
<mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>>>>>
wrote:
>>
>> Hi Vitaly,
>> I did it because I read from
>>
http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
>> that says:
>> "One solution is to simply comment out
(or delete)
the lines
of code out
>> in the file where it is included for the
second time
i.e.,
..". So if it is
>> the case I am going to undo it to see what
happens...
I will
let you know.
>> Thanks/Jamie
>> On Mon, Aug 10, 2009 at 5:05 PM, Vitaly
V. Chaban
<vvcha...@gmail.com
<mailto:vvcha...@gmail.com> <mailto:vvcha...@gmail.com
<mailto:vvcha...@gmail.com>>
<mailto:vvcha...@gmail.com <mailto:vvcha...@gmail.com>
<mailto:vvcha...@gmail.com <mailto:vvcha...@gmail.com>>>
<mailto:vvcha...@gmail.com
<mailto:vvcha...@gmail.com> <mailto:vvcha...@gmail.com
<mailto:vvcha...@gmail.com>>
<mailto:vvcha...@gmail.com <mailto:vvcha...@gmail.com>
<mailto:vvcha...@gmail.com <mailto:vvcha...@gmail.com>>>>>
>> wrote:
>>>
>>> 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.
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-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> <http://vt.edu/>
<http://vt.edu/> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> <http://vt.edu/> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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