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

[Justin A. Lemkul]

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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