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

[Justin A. Lemkul]

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

========================================