[gmx-users] problems in setup the protein+ membrane

[Mark Abraham]

On 12/02/10 18:17, chiloo777 777 wrote:
> If this problem comes from the mismatch forcefield, That mean i should
> change forcefield from ffG53a6 to ffgmx, or find popg.itp (which is
> matched with ffG53a6), right?

Standard procedure is to choose a forcefield that is known to be able to 
model the kind of system you're working on before you do anything else :-)

Mark

> On Fri, Feb 12, 2010 at 9:06 AM, Justin A. Lemkul<jalemkul at vt.edu>  wrote:
>>
>>
>> chiloo777 777 wrote:
>>>
>>> To see topology, please see the attached files
>>>
>>
>> You're using ffG53a6, per my tutorial, but then if you look within popg.itp,
>> you'll find atom type HO, which is not a recognized type within 53a6 (it is
>> for ffgmx).  The proper type is H.  The other warnings are probably due to
>> some other similar force field type mismatch.  Identify which of these is
>> problematic (grompp should print the line number in the topology), and
>> assign suitable parameters.
>>
>> As for this:
>>
>> ; Include water topology
>> #include "#include "/usr/local/gromacs/share/top/flexspc.itp"
>>
>> I have no idea how that would even work, you don't even have proper closed
>> quotes, but in any case you would only ever need:
>>
>> #include "flexspc.itp"
>>
>> ...although you shouldn't be using a flexible water model for dynamics,
>> anyway.
>>
>> -Justin
>>
>>> Jit
>>>
>>> On Fri, Feb 12, 2010 at 8:45 AM, Justin A. Lemkul<jalemkul at vt.edu>  wrote:
>>>>
>>>> chiloo777 777 wrote:
>>>>>
>>>>> Do you mean i should change the order of #include thing in file.top or
>>>>>   something involving pope.itp?
>>>>> I try to change order of #include thing, there is the same error.
>>>>> Do i need to define something like "proper dihedral types" in pope.itp
>>>>> &  popg.itp?
>>>>>
>>>> Without seeing your .top it's hard to give any really useful information.
>>>>   All the bonded parameters for a given lipid should be included within
>>>> the
>>>> relevant .itp file.  If it's coming up as "not found" you're either using
>>>> the wrong force field, not #including something at all, or your topology
>>>> is
>>>> otherwise incorrectly constructed.
>>>>
>>>> -Justin
>>>>
>>>>> Thanks
>>>>> Jit
>>>>>
>>>>> On Fri, Feb 12, 2010 at 8:24 AM, Mark Abraham<Mark.Abraham at anu.edu.au>
>>>>> wrote:
>>>>>>
>>>>>> On 12/02/10 12:16, chiloo777 777 wrote:
>>>>>>>
>>>>>>> Dear all,
>>>>>>>
>>>>>>> I face some problem during run grompp (see below), the command is
>>>>>>> "grompp -f em.mdp -c ../2add_lipw/b4ion.gro -p ../topol.top -o
>>>>>>> b4ion.tpr"
>>>>>>>
>>>>>>> -Before this process, i've changed the ffG53a6nb.itp&    ff53Ga6bon.itp
>>>>>>> according to the tutorial
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html)
>>>>>>>
>>>>>>> my topology, you can see the attached files.
>>>>>>> Thanks in advance
>>>>>>> Jit
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --------------------------------------------------------------------------------------------
>>>>>>> Ignoring obsolete mdp entry 'cpp'
>>>>>>>
>>>>>>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
>>>>>>> checking input for internal consistency...
>>>>>>> processing topology...
>>>>>>> Opening library file /usr/local/gromacs/share/top/ff_dum.itp
>>>>>>> Generated 825 of the 2346 non-bonded parameter combinations
>>>>>>>
>>>>>>> ERROR 1 [file /home/jit/Lipid_Bilayers/pope.itp, line 234]:
>>>>>>>   No default Proper Dih. types
>>>>>>
>>>>>> If there's no default proper dihedral types defined, then you've
>>>>>> #included
>>>>>> things in a wrong order.
>>>>>>
>>>>>> Mark
>>>>>>
>>>>>>> -------------------------------------------------------
>>>>>>> Program grompp, VERSION 4.0.7
>>>>>>> Source code file: toppush.c, line: 947
>>>>>>>
>>>>>>> Fatal error:
>>>>>>> Atomtype HO not found
>>>>>>> -------------------------------------------------------
>>>>>>>
>>>>>>> "There's Nothing We Can't Fix, 'coz We Can Do It in the Mix" (Indeep)
>>>>>>>
>>>>>>>
>>>>>> --
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>>>>>>
>>>>>
>>>>>
>>>> --
>>>> ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Ph.D. Candidate
>>>> ICTAS Doctoral Scholar
>>>> MILES-IGERT Trainee
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]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
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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