[gmx-users] Regarding engineered residue topology

Justin Lemkul jalemkul at vt.edu
Tue Jul 28 15:55:12 CEST 2015 


On 7/28/15 8:48 AM, Venkat Reddy wrote:
> Thanks Justin. How shall I tackle this problem? Can I use any other AA
> force field, say CHARMM27?

Use any force field you like that has suitable parameters and will adequately 
address the desired simulation.

> The Aib parameters are available in an old gromacs forcefield (mentioned as
> "DEPRECATED" in gromacs-4.5.7), which hasn't showed any error while
> simulating the same system.
>

One should not use ffgmx (hacked GROMOS87, not to be called "GROMACS force 
field," even though people unfortunately do).

-Justin

> On Tue, Jul 28, 2015 at 6:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 7/28/15 3:30 AM, Venkat Reddy wrote:
>>
>>> Thank you Justin for clear explanation.
>>> However, the parameters are available for
>>> CX     CT     CT_2   HC      3      0.96650   2.89951   0.00000  -3.86601
>>> 0.000   0.000;
>>> C*     CT     CT_2   HC      3      0.96650   2.89951   0.00000  -3.86601
>>> 0.000   0.000 ;
>>> So, can I apply the same for CT-CT_2-CT-HC dihedral?
>>>
>>>
>> No idea.  Generally dihedrals are the least transferable of any bonded
>> parameter, so there's no reason to assume that you can apply the parameters
>> from other interactions to any other given interaction.
>>
>> -Justin
>>
>>
>>   Thank you for your valuable time and concern.
>>>
>>> On Mon, Jul 27, 2015 at 5:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 7/27/15 1:21 AM, Venkat Reddy wrote:
>>>>
>>>>   Dear Justin,
>>>>> Thank you for the prompt reply. I have checked the topology file once
>>>>> again
>>>>> and confirmed the dihedral (CB2-CA-CB1-HB11) thats creating problem. The
>>>>> Aib parameters are indeed available for OPLS-AA ff. But I couldn't
>>>>> locate
>>>>> the dihedral parameters for the above mentioned dihedral angle in
>>>>> ffbonded.itp file. However I found dihedral parameters for X-CA-CB-X.
>>>>> So,
>>>>> can I use X-CA-CB-X parameters for CB2-CA-CB1-HB11 dihedral?
>>>>>
>>>>>
>>>>>   You're confusing atom names and atom types.  The names are totally
>>>> irrelevant for parameter assignment.  The CB2-C1-CB1-HB11 dihedral has a
>>>> sequence of nonbonded types of opls_135-opls_225B-opls_135-opls_140,
>>>> which
>>>> have bonded types (see second column of ffnonbonded.itp) of
>>>> CT-CT_2-CT-HC.
>>>> So the parameters you need are for CT-CT_2-CT-HC, which are indeed not in
>>>> ffbonded.itp.
>>>>
>>>> -Justin
>>>>
>>>>
>>>>    On Mon, Jul 27, 2015 at 5:46 AM, Justin Lemkul <jalemkul at vt.edu>
>>>> wrote:
>>>>
>>>>>
>>>>>
>>>>>
>>>>>> On 7/24/15 9:20 AM, Venkat Reddy wrote:
>>>>>>
>>>>>>    Dear all,
>>>>>>
>>>>>>> I am trying to simulate a peptide with engineered residues like Aib
>>>>>>> (alpha
>>>>>>> amino-isobutyric acid). I am trying to use OPLS-aa forcefield. Though
>>>>>>> everything went well initially during topology generation, grompp
>>>>>>> showed
>>>>>>> the following error.
>>>>>>>
>>>>>>> ERROR 1 [file topol.top, line 2316]:
>>>>>>>       No default Ryckaert-Bell. types
>>>>>>> ERROR 2 [file topol.top, line 2317]:
>>>>>>>       No default Ryckaert-Bell. types
>>>>>>> ERROR 3 [file topol.top, line 2318]:
>>>>>>>       No default Ryckaert-Bell. types
>>>>>>> ERROR 4 [file topol.top, line 2325]:
>>>>>>>       No default Ryckaert-Bell. types
>>>>>>> ERROR 5 [file topol.top, line 2326]:
>>>>>>>       No default Ryckaert-Bell. types
>>>>>>> ERROR 6 [file topol.top, line 2327]:
>>>>>>>       No default Ryckaert-Bell. types
>>>>>>>
>>>>>>> The cross-check with topolo.top identified the dihedral
>>>>>>> CB2-CA-CB1-HB11
>>>>>>> is
>>>>>>> throwing the error. My question is, even though the parameters for Aib
>>>>>>> are
>>>>>>> available in OPLS ff, why I am getting this error?
>>>>>>>
>>>>>>>
>>>>>>>    grompp doesn't lie.  Either you're looking at the wrong lines or
>>>>>>> you're
>>>>>>>
>>>>>> looking at the wrong parameters.  Some residues are constructed for
>>>>>> convenience but if they're not "official" then there may be problems.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>> --
>>>>>> ==================================================
>>>>>>
>>>>>> Justin A. Lemkul, Ph.D.
>>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>>
>>>>>> Department of Pharmaceutical Sciences
>>>>>> School of Pharmacy
>>>>>> Health Sciences Facility II, Room 629
>>>>>> University of Maryland, Baltimore
>>>>>> 20 Penn St.
>>>>>> Baltimore, MD 21201
>>>>>>
>>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>>
>>>>>> ==================================================
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
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>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>   --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>
>>>> Department of Pharmaceutical Sciences
>>>> School of Pharmacy
>>>> Health Sciences Facility II, Room 629
>>>> University of Maryland, Baltimore
>>>> 20 Penn St.
>>>> Baltimore, MD 21201
>>>>
>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>
>>>> ==================================================
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>>>> Gromacs Users mailing list
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>>>
>>>
>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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>> Gromacs Users mailing list
>>
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>
>
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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

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