[gmx-users] Re: itp file
Jamie Seyed
jamie.seyed at gmail.com
Tue Aug 11 02:40:03 CEST 2009
First I put 1000, but after editconf and genbox it has been changed to 572.
I only have 1 part with SOL 572...
On Mon, Aug 10, 2009 at 8:36 PM, Justin A. Lemkul <jalemkul at 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 <jalemkul at vt.edu<mailto:
>> jalemkul at 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
>> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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.seyed at gmail.com <mailto:jamie.seyed at gmail.com>
>> <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
>> <mailto:jamie.seyed at gmail.com
>> <mailto:jamie.seyed at gmail.com> <mailto:jamie.seyed at gmail.com
>> <mailto:jamie.seyed at 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
>> <vvchaban at gmail.com <mailto:vvchaban at gmail.com>
>> <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>>
>> <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>
>> <mailto:vvchaban at gmail.com <mailto:vvchaban at 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.seyed at gmail.com
>> <mailto:jamie.seyed at gmail.com>
>> <mailto:jamie.seyed at gmail.com
>> <mailto:jamie.seyed at gmail.com>> <mailto:jamie.seyed at gmail.com
>> <mailto:jamie.seyed at gmail.com>
>>
>> <mailto:jamie.seyed at gmail.com
>> <mailto:jamie.seyed at 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.seyed at gmail.com
>> <mailto:jamie.seyed at gmail.com> <mailto:jamie.seyed at gmail.com
>> <mailto:jamie.seyed at gmail.com>>
>> <mailto:jamie.seyed at gmail.com
>> <mailto:jamie.seyed at gmail.com> <mailto:jamie.seyed at gmail.com
>> <mailto:jamie.seyed at 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
>> <vvchaban at gmail.com <mailto:vvchaban at gmail.com>
>> <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>>
>> <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>
>> <mailto:vvchaban at gmail.com <mailto:vvchaban at 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 at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> <mailto:gmx-users at gromacs.org
>> <mailto:gmx-users at 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-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>
>> <mailto:gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at 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/> <http://vt.edu/> | (540)
>> 231-9080
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>>
>>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/searchbefore
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www
>> interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>
>> <mailto:gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at 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 at gromacs.org
>> <mailto:gmx-users at 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-request at gromacs.org
>> <mailto:gmx-users-request at 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 at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090810/7b631dab/attachment.html>
More information about the gromacs.org_gmx-users
mailing list