[gmx-users] Re: itp file
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Aug 11 02:36:47 CEST 2009
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 <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>> 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>>>
>>> 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>>> 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>>> 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>>>
>>> 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>>>
>>>
>>> >> 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/> | (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 | (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
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>
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