[gmx-users] Regarding engineered residue topology
Venkat Reddy
venkat4bt at gmail.com
Tue Jul 28 14:48:58 CEST 2015
Thanks Justin. How shall I tackle this problem? Can I use any other AA
force field, say CHARMM27?
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.
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
>
> ==================================================
> --
> Gromacs Users mailing list
>
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--
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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