[gmx-users] NMR restrained MD
Justin Lemkul
jalemkul at vt.edu
Tue Sep 10 22:16:30 CEST 2013
On 9/10/13 3:54 PM, Rafael I. Silverman y de la Vega wrote:
> How so? If there is an atom type that has a reasonable similarity to the
> one that doesnt have the default bondtypes, what makes using that worse
> than coming up with entirely new parameters that are not necessarily based
> on physical data or quantum calculations? Isnt copying angles and force
> constants the same thing?
>
I never suggested that one should make up parameters that aren't based on
anything. The nonbonded parameters of any force field are highly tuned for
internal consistency, so I was alarmed at the suggestion of simply replacing
atom types. Doing so can very easily perturb the model physics in unpredictable
ways.
Perhaps I should have stated more clearly from the beginning - I never meant to
imply that anyone should simply "add parameters" for a missing interaction.
They must be properly derived. I do maintain (having seen the negative
consequences myself from others' struggles and failed attempts) that replacing
atom types for mere convenience leads to very bad outcomes, probably just as bad
as poorly concocted bonded parameters, if not worse.
It should also be noted that the nonbonded parameters affect torsions, so all of
these terms are, in reality, interrelated. I suspect that the underlying issue
here has been a poorly constructed force field, not parameters that are actually
missing from the model.
-Justin
>
> On Tue, Sep 10, 2013 at 10:34 AM, 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
>>>>>>
>>>>>> jalemkul at outerbanks.umaryland.******edu <jalemkul at outerbanks.**
>>>>>> umaryland.edu <jalemkul at outerbanks.**umaryland.edu<jalemkul at outerbanks.umaryland.edu>>>
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>>>>>> 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 <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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--
==================================================
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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