[gmx-users] NMR restrained MD
Rama Krishna Koppisetti
ramkishna72 at gmail.com
Tue Sep 10 21:55:57 CEST 2013
Hi Justin,
There is no errors in dihedral but I got 4 warnings in ffbonded.itp. Is
there any suggestions from you.
WARNING 1 [file ffbonded.itp, line 2817]:
Overriding Proper Dih. parameters.
Use dihedraltype 4 to allow several multiplicity terms.
old: 180 5.86 1 180 5.86 1
new: LNL LH2 LC2 LOS 1 0.00 8.62 3
WARNING 2 [file ffbonded.itp, line 2820]:
Overriding Proper Dih. parameters.
Use dihedraltype 4 to allow several multiplicity terms.
old: 0 5.09 2 0 5.09 2
new: LC2 LOS LP LOS 1 0.00 3.19 3
WARNING 3 [file ffbonded.itp, line 2821]:
Overriding Proper Dih. parameters.
Use dihedraltype 4 to allow several multiplicity terms.
old: 0 3.19 3 0 3.19 3
new: LOS LP LOS LC2 1 0.00 5.09 2
WARNING 4 [file ffbonded.itp, line 2822]:
Overriding Proper Dih. parameters.
Use dihedraltype 4 to allow several multiplicity terms.
old: 0 5.09 2 0 5.09 2
new: LOS LP LOS LC2 1 0.00 3.19 3
Thanks
--Rama
On Tue, Sep 10, 2013 at 12:34 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 9/10/13 1:28 PM, Rafael I. Silverman y de la Vega wrote:
>
>> Adding parameters can be a little bit of a pain, you could instead change
>> the atom types in the molecule parameter, to ones that have defined angles
>> and bond types with each other. Of course, you would need to make sure
>> that
>> you dont assign sp2 with sp3 atoms, or aromatic with non aromatic etc.
>> Check out ffbonded in the appropriate forcefield folder to see which
>> atomtypes have defined bond types. Check out atomtypes.atp to see all the
>> atom types for the forcefield
>>
>>
> Given that at present the issue involves only protein and lipids, the
> approach of swapping around atom types is very dangerous, probably more so
> than assigning bonded parameters by analogy. I don't recall the OP ever
> telling us what the force field is, though, so it's hard to know all of
> what we're dealing with here.
>
>
> -Justin
>
>
>> On Tue, Sep 10, 2013 at 6:40 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 9/10/13 9:33 AM, Rama Krishna Koppisetti wrote:
>>>
>>> Hi Justin,
>>>>
>>>> It is which part in the force field. Exactly which file I have to look
>>>> to
>>>> overcome this errors.
>>>>
>>>>
>>>> Go to the line number in the .top indicated in the error message and
>>> determine the atom types. This will tell you the sequence of atom types
>>> involved in the R-B dihedral that is missing. In theory, you would then
>>> add missing parameters to ffbonded.itp, if they exist.
>>>
>>> -Justin
>>>
>>>
>>> On Tue, Sep 10, 2013 at 8:25 AM, Justin Lemkul <jalemkul at vt.edu>
>>> wrote:
>>>
>>>>
>>>>
>>>>
>>>>> On 9/10/13 9:21 AM, Rama Krishna Koppisetti wrote:
>>>>>
>>>>> Hi Justin,
>>>>>
>>>>>>
>>>>>> This is another type of error while running energy minimization:
>>>>>> what to do for these type of errors.
>>>>>>
>>>>>>
>>>>>> They're exactly the same as the dihedral error from before. You're
>>>>>>
>>>>> using
>>>>> parameters that don't exist in the force field.
>>>>>
>>>>> -Justin
>>>>>
>>>>> ERROR 218 [file topol.top, line 23487]:
>>>>>
>>>>> No default Ryckaert-Bell. types
>>>>>>
>>>>>>
>>>>>> ERROR 219 [file topol.top, line 23499]:
>>>>>> No default Ryckaert-Bell. types
>>>>>>
>>>>>>
>>>>>> ERROR 220 [file topol.top, line 23500]:
>>>>>> No default Ryckaert-Bell. types
>>>>>>
>>>>>>
>>>>>> ERROR 221 [file topol.top, line 23501]:
>>>>>> No default Ryckaert-Bell. types
>>>>>>
>>>>>>
>>>>>> ERROR 222 [file topol.top, line 23502]:
>>>>>> No default Ryckaert-Bell. types
>>>>>>
>>>>>>
>>>>>> ERROR 223 [file topol.top, line 23503]:
>>>>>> No default Ryckaert-Bell. types
>>>>>>
>>>>>>
>>>>>> ERROR 224 [file topol.top, line 23515]:
>>>>>> No default Ryckaert-Bell. types
>>>>>>
>>>>>>
>>>>>> --Rama
>>>>>>
>>>>>>
>>>>>> On Mon, Sep 9, 2013 at 5:16 PM, Justin Lemkul <jalemkul at vt.edu>
>>>>>> wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote:
>>>>>>>
>>>>>>> Hi Justin,
>>>>>>>
>>>>>>>
>>>>>>>> I included 1 DMPC molecule parameters in the file should I need to
>>>>>>>> include
>>>>>>>> 128 molecules parameters in the file .rtp.
>>>>>>>>
>>>>>>>>
>>>>>>>> No. Residue definitions are used any time they are encountered
>>>>>>>> in
>>>>>>>> the
>>>>>>>>
>>>>>>>> coordinate file. There is no need for such redundancy at the force
>>>>>>> field
>>>>>>> level.
>>>>>>>
>>>>>>>
>>>>>>> -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 <jalemkul at outerbanks.**
>>>>>>> umaryland.edu <jalemkul at outerbanks.**umaryla**nd.edu<http://umaryland.edu>
>>>>>>> <jalemkul at outerbanks.**umaryland.edu<jalemkul at outerbanks.umaryland.edu>
>>>>>>> >>>
>>>>>>> | (410)
>>>>>>> 706-7441
>>>>>>>
>>>>>>> ==============================********====================
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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
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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 <jalemkul at outerbanks.**
>>> umaryland.edu <jalemkul at outerbanks.umaryland.edu>> | (410)
>>> 706-7441
>>>
>>> ==============================****====================
>>>
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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 <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
>
> ==============================**====================
>
> --
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