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

[chiloo777 777]

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?

Thanks
Jit

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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