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

chiloo777 777 chiloo777 at gmail.com
Fri Feb 12 13:31:35 CET 2010 

Thanks for Your suggestion, I will use an updated forcefield &
gradually adjust each error lines.

Jit

On Fri, Feb 12, 2010 at 6:50 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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 things...be sure you can justify your use of this outdated force field.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
>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>>>>> Please search the archive at http://www.gromacs.org/search before
>>>>>>>>> posting!
>>>>>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>>>>>> interface
>>>>>>>>> or send it to gmx-users-request at gromacs.org.
>>>>>>>>> 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
>>>>>>>
>>>>>>> ========================================
>>>>>>> --
>>>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>>> Please search the archive at http://www.gromacs.org/search before
>>>>>>> posting!
>>>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>>>> interface
>>>>>>> or send it to gmx-users-request at gromacs.org.
>>>>>>> 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
>>>>>
>>>>> ========================================
>>>>> --
>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> Please search the archive at http://www.gromacs.org/search before
>>>>> posting!
>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>> interface
>>>>> or send it to gmx-users-request at gromacs.org.
>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>
>>>>
>>>>
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface
>>> or send it to gmx-users-request at gromacs.org.
>>> 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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Other mails:
chiloo7 at hotmail.com
chiloo77 at yahoo.com
lchitt at kku.ac.th

More information about the gromacs.org_gmx-users mailing list