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

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 12 12:50:53 CET 2010 


chiloo777 777 wrote:
> So, I've changed forcefield from ffG53a6 to ffgmx, the errors are as
> following lines.
> Please suggest me, how can i remove such errors.
> 

Well, an arbitrary change to a deprecated force field just to get around a 
simple atom type mismatch may or may not be the best way to handle things...be 
sure you can justify your use of this outdated force field.  If your 
justification is "to make errors go away," be sure you're ready for reviewer 
criticism.  There have been many lively and informative debates over this list 
(some in recent weeks) about which parameter sets should and should not be used 
for membrane protein simulation, so I would encourage you to do a few minutes of 
searching in the archives.

> 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
> 

As I said before, look up what's on this line, see what atoms it corresponds to, 
and try to figure out why the error is coming up.  The line number in the file 
is even printed for you, you just have to map back which atoms are affected.

-Justin

> 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
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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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>>>
>>>
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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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