[gmx-users] OPLS force field issue....
Sidath Wijesinghe
swijesi at g.clemson.edu
Fri Dec 20 20:48:16 CET 2013
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
>>>>>>>
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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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>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>> ==================================================
>>>
>>> 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.
>>>
>>>
>>
>>
>>
> --
> ==================================================
>
> 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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>
--
Sidath Wijesinghe
Graduate Teaching Assistant
Dept Of Chemistry
Clemson University
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