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

chiloo777 777 chiloo777 at gmail.com
Fri Feb 12 10:47:59 CET 2010 

So, I've changed forcefield from ffG53a6 to ffgmx, the errors are as
following lines.
Please suggest me, how can i remove such errors.

Thanks
Jit

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs/share/top/ffgmxnb.itp
Opening library file /usr/local/gromacs/share/top/ffgmxbon.itp
Opening library file /usr/local/gromacs/share/top/ff_dum.itp
Generated 1174 of the 2016 non-bonded parameter combinations

ERROR 1 [file /DATA/jit/ff53a6/pope.itp, line 234]:
  No default Proper Dih. types

Excluding 3 bonded neighbours molecule type 'Protein_A'
Excluding 3 bonded neighbours molecule type 'POPE'
Excluding 3 bonded neighbours molecule type 'DPOPG'
Excluding 3 bonded neighbours molecule type 'LPOPG'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'Na'

NOTE 1 [file ../topol.top, line 2359]:
  System has non-zero total charge: 2.600001e+01



processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...

There was 1 note

-------------------------------------------------------
Program grompp, VERSION 4.0.7
Source code file: grompp.c, line: 986

Fatal error:
There was 1 error in input file(s)
-------------------------------------------------------

"Disturb the Peace of a John Q Citizen" (Urban Dance Squad)



On Fri, Feb 12, 2010 at 2:49 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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)
>>>>>>>>
>>>>>>>>
>>>>>>> --
>>>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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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
>>>>>
>>>>> ========================================
>>>>> --
>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>
>>>>
>>>>
>>>>
>>>
>>> --
>>> ========================================
>>>
>>> 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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>>
>>
>>
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