The gro file:
-------------------------
GROtesk MACabre and Sinister
1836
12 C 1 1.311 1.563 0.994
12 C 2 1.220 1.635 1.079
12 C 3 1.092 1.565 1.081
12 C 4 1.108 1.449 0.996
.........
12 H 118 1.438 1.092 1.244
12 H 119 1.413 1.098 1.426
12 H 120 1.291 1.033 1.329
2SOL OW 121 0.569 1.275 1.165
2SOL HW1 122 0.476 1.268 1.128
2SOL HW2 123 0.580 1.364 1.209
.......
572SOL HW2 1833 2.024 1.991 2.158
573SOL OW 1834 2.290 2.286 2.382
573SOL HW1 1835 2.320 2.214 2.320
573SOL HW2 1836 2.251 2.246 2.465
2.64467 2.64467 2.64467
-----------------------------------------
and itp-file:
-----------------
; Include forcefield parameters
[ moleculetype ]
; Name nrexcl
C60CH3 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 opls_145 1 C60CH3 C 1 0
12.011 ; qtot 0
2 opls_516 1 C60CH3 C 2 0
12.011 ; qtot 0
.....
71 78 79 69 3 1.740000e+02 5.000000e+00 3.000000e+00
1.740000e+02 5.000000e+00 3.000000e+00
69 79 80 2 3 2.580000e+02 5.000000e+00 3.000000e+00
2.580000e+02 5.000000e+00 3.000000e+00
[ system ]
; Name
C60CH3
[ molecules ]
; Compound #mols
C60CH3 1
-----------------------------------------------
Oh Ok now I understand that I should remove only one of the [molecule]
sections in itp-file (right)??
Thanks a lot/ Please let me know if still something is
missing.../Thanks/Jamie
On Mon, Aug 10, 2009 at 8:42 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Jamie Seyed wrote:
First I put 1000, but after editconf and genbox it has been
changed to 572. I only have 1 part with SOL 572...
I'm thoroughly confused. There is no need to manually manipulate
these sections if you're allowing genbox, genion, etc to manipulate
them for you. Please post the following information to get a
resolution:
1. Your .top file
2. Your molecule.itp file (you can delete out lines in the atoms,
bonds, dihedrals section so the file is not unnecessarily long - I'm
really just interested in the other directives that may be present)
-Justin
On Mon, Aug 10, 2009 at 8:36 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,
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>>
<mailto: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>>>
<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 <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>>>>
<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
<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>>>>
<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 <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>>>> <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
<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>>>>
<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
<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>>>>
<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 <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/>
<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/>
<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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