[gmx-users] OPLS force field issue....

Fri Jan 10 21:28:10 CET 2014

Justin,

i was able to  obtain the . top file for 3 uncharged monomers. then i used
the grompp

i got a fatal error as follows....

Program grompp, VERSION 4.5.5
Source code file: grompp.c, line: 175

Fatal error:
The largest charge group contains 207 atoms. The maximum is 32.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

what could be the reason for this? do you think i have done some thing
wrong?
could you please help me out.

Thank you!
Sidath

On Fri, Dec 20, 2013 at 2:48 PM, Sidath Wijesinghe <swijesi at g.clemson.edu>wrote:

> yes that was the .top file i have used. ok..
>
> Thank you!
>
>
> On Fri, Dec 20, 2013 at 2:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 12/20/13 2:20 PM, Sidath Wijesinghe wrote:
>>
>>> Justin,
>>>
>>> i went for the option 4 that u pointed out. let me explain what i did,
>>>
>>> i converted the .pdb file in to .gro by using.
>>>
>>> editconf -f test.pdb -o test.gro -box 18 18 18 -angles 90 90 90
>>>
>>> then i use the text editor as follows.
>>>
>>>
>>> Include forcefield parameters
>>> #include "oplsaa.ff/forcefield.itp"
>>> #include "oplsaa.ff/ions.itp"
>>> [ moleculetype ]
>>> ; name  nrexcl
>>>    UNK     3
>>>
>>> then i did
>>>
>>>   grompp -f npt.mdp -c test.gro -p test.top -o run.tpr
>>>
>>> and i got following error...
>>>
>>> Program grompp, VERSION 4.5.5
>>> Source code file: grompp.c, line: 479
>>>
>>> Fatal error:
>>> No molecules were defined in the system
>>>
>>> could you please help me out here? am i doing it correct?
>>>
>>>
>> No.  If that's actually the entirety of the topology, it basically
>> contains nothing.  You're missing 99.9% of the required information.
>>
>> -Justin
>>
>>
>>  Thank you!
>>>
>>>
>>> On Thu, Dec 19, 2013 at 8:01 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 12/18/13 10:13 PM, Sidath Wijesinghe wrote:
>>>>
>>>>  could you please give me a hint about a suitable method for this task?
>>>>>
>>>>>
>>>>>  You can make just about anything work.
>>>>
>>>> 1. pdb2gmx with .rtp entries for each of your molecules, with
>>>> appropriately named (unique) atoms
>>>> 2. g_x2top can also process each different molecule type, yielding
>>>> topologies for each of them individually.  Conversion from .top to .itp
>>>> is
>>>> trivial.
>>>> 3. Software of your own creation
>>>> 4. Chapter 5 of the manual and your favorite text editor (laborious, but
>>>> works well if you know what you are doing)
>>>>
>>>> -Justin
>>>>
>>>>
>>>>   thank you!
>>>>
>>>>>
>>>>>
>>>>> On Wed, Dec 18, 2013 at 9:50 PM, Justin Lemkul <jalemkul at vt.edu>
>>>>> wrote:
>>>>>
>>>>>
>>>>>
>>>>>> On 12/18/13 9:46 PM, Sidath Wijesinghe wrote:
>>>>>>
>>>>>>      Is g_x2top  the only way for my situation? or am i in the wrong
>>>>>>
>>>>>>> track?
>>>>>>>
>>>>>>>
>>>>>>>   There are numerous ways to generate topologies.  I have warned you
>>>>>>> that
>>>>>>>
>>>>>> g_x2top is probably ill-suited for this task.  It works well for
>>>>>> simple
>>>>>> things.  It does not work well for complex systems.
>>>>>>
>>>>>>
>>>>>>    if i find the parameters for the missing parameters how can i get
>>>>>> rid
>>>>>> of
>>>>>>
>>>>>>  sodium as u mentioned
>>>>>>> for the real system with Na+ ions?
>>>>>>>
>>>>>>>
>>>>>>>   I answered this question in my previous message.
>>>>>>>
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>
>>>>>>    Thank you!
>>>>>>
>>>>>>
>>>>>>>
>>>>>>> On Wed, Dec 18, 2013 at 9:37 PM, Justin Lemkul <jalemkul at vt.edu>
>>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>  On 12/18/13 9:32 PM, Sidath Wijesinghe wrote:
>>>>>>>>
>>>>>>>>    Justin,
>>>>>>>>
>>>>>>>>
>>>>>>>>> As i understood from reading and tutorial what i should do is, lets
>>>>>>>>> say
>>>>>>>>> i
>>>>>>>>> generated a topology file named as
>>>>>>>>> topol.top, so i need to add #include "oplsaa.ff/ions.itp" so it
>>>>>>>>> accounts
>>>>>>>>> for Na+.
>>>>>>>>>
>>>>>>>>> my question is..
>>>>>>>>>
>>>>>>>>> 1.how can i get rid of sodium? just removing the corresponding
>>>>>>>>> lines
>>>>>>>>> from
>>>>>>>>> the .pdb text?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>   Yes, for the coordinate file processed by g_x2top.  Once the
>>>>>>>>>
>>>>>>>> topology for
>>>>>>>> everything else is established and you have #included the topology
>>>>>>>> for
>>>>>>>> sodium (as I explained before), you can use the original coordinate
>>>>>>>> file.
>>>>>>>>
>>>>>>>>
>>>>>>>>     2. i tried with uncharged system for simplicity with less
>>>>>>>> number of
>>>>>>>>
>>>>>>>>   atoms..(
>>>>>>>>
>>>>>>>>> here i replaced the COONa functional group with a CH3 group)
>>>>>>>>>
>>>>>>>>> but still g_x2top -f test.pdb -o np1.top -name np1 -ff oplsaa -pbc
>>>>>>>>>
>>>>>>>>> am getting this parameters missing..
>>>>>>>>>
>>>>>>>>> Can not find forcefield for atom C-147 with 1 bonds
>>>>>>>>> Can not find forcefield for atom C-148 with 1 bonds
>>>>>>>>> Can not find forcefield for atom C-873 with 1 bonds
>>>>>>>>> Can not find forcefield for atom C-874 with 1 bonds
>>>>>>>>> Can not find forcefield for atom C-939 with 1 bonds
>>>>>>>>> Can not find forcefield for atom C-940 with 1 bonds
>>>>>>>>> Can not find forcefield for atom C-1137 with 1 bonds
>>>>>>>>> Can not find forcefield for atom C-1138 with 1 bonds
>>>>>>>>> Can not find forcefield for atom C-1269 with 1 bonds
>>>>>>>>> Can not find forcefield for atom C-1270 with 1 bonds
>>>>>>>>>
>>>>>>>>> for that do i need to modify the atomname2type.n2t  the way i did
>>>>>>>>> earlier?or am i doing this wrong?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>    g_x2top is not very smart.  You have to give it all the
>>>>>>>>> information
>>>>>>>>>
>>>>>>>>>  needed
>>>>>>>> for it to work.  Whenever you get this error, the solution is always
>>>>>>>> the
>>>>>>>> same - those atoms are not accounted for by whatever is in the .n2t
>>>>>>>> file,
>>>>>>>> so you need to add information to cover those atoms.
>>>>>>>>
>>>>>>>> -Justin
>>>>>>>>
>>>>>>>> --
>>>>>>>> ==================================================
>>>>>>>>
>>>>>>>>
>>>>>>>> Justin A. Lemkul, Ph.D.
>>>>>>>> Postdoctoral Fellow
>>>>>>>>
>>>>>>>> Department of Pharmaceutical Sciences
>>>>>>>> School of Pharmacy
>>>>>>>> Health Sciences Facility II, Room 601
>>>>>>>> University of Maryland, Baltimore
>>>>>>>> 20 Penn St.
>>>>>>>> Baltimore, MD 21201
>>>>>>>>
>>>>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>>>>>
>>>>>>>> ==================================================
>>>>>>>>
>>>>>>>> --
>>>>>>>> Gromacs Users mailing list
>>>>>>>>
>>>>>>>> * Please search the archive at http://www.gromacs.org/
>>>>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>>>>>>
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>>>>>>>>
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>>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor
>>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>   --
>>>>>>>
>>>>>> ==================================================
>>>>>>
>>>>>> Justin A. Lemkul, Ph.D.
>>>>>> Postdoctoral Fellow
>>>>>>
>>>>>> Department of Pharmaceutical Sciences
>>>>>> School of Pharmacy
>>>>>> Health Sciences Facility II, Room 601
>>>>>> University of Maryland, Baltimore
>>>>>> 20 Penn St.
>>>>>> Baltimore, MD 21201
>>>>>>
>>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>>>
>>>>>> ==================================================
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at http://www.gromacs.org/
>>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>>>>
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>
>>>>>> * For (un)subscribe requests visit
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>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>  --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Postdoctoral Fellow
>>>>
>>>> Department of Pharmaceutical Sciences
>>>> School of Pharmacy
>>>> Health Sciences Facility II, Room 601
>>>> University of Maryland, Baltimore
>>>> 20 Penn St.
>>>> Baltimore, MD 21201
>>>>
>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>
>>>> ==================================================
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at http://www.gromacs.org/
>>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>>
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>>>>
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>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>>
>>>
>>>
>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
>
> --
> Sidath Wijesinghe
> Graduate Teaching Assistant
> Dept Of Chemistry
> Clemson University
>
>

-- 
Sidath Wijesinghe
Graduate Teaching Assistant
Dept Of Chemistry
Clemson University