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...??/ Thank you in
advance.../Jamie
Make sure you have only one [ molecules ] section. I think Justin's
probably picked your problem, inasmuch as you've just renamed a
molecule.top to molecule.itp without removing the directives that should
not be in an .itp file.
Mark
On Mon, Aug 10, 2009 at 8:20 PM, Justin A. Lemkul <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>> 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>>>
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>>> 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>>> 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>>>
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>>>
>> 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.
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- ========================================
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
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
