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

[chiloo777 777]

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?

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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