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

Justin Lemkul jalemkul at vt.edu
Fri Dec 20 20:25:39 CET 2013



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/
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>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>   --
>>>> ==================================================
>>>>
>>>> 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/
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>>>>
>>>
>>>
>>>
>> --
>> ==================================================
>>
>> 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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>>
>
>
>

-- 
==================================================

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

==================================================


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