[gmx-users] No default Ryckaert-Bell. types for proline

[Justin Lemkul]

On 6/1/15 12:25 PM, Kevin C Chan wrote:
> pdb2gmx command:
> gmx_d pdb2gmx -f proline.pdb -ter > 15: (OPLS-AA/L all-atom force field
> (2001 aminoacid dihedrals)) > 1: TIP4P  TIP 4-point, recommended > 1:
> PRO-ZWITTERION_NH2+ (only use with zwitterions containing exactly one
> residue) > 1: PRO-ZWITTERION_COO- (only use with zwitterions containing
> exactly one residue)
>
> (I have also tried 4: ZWITTERION_NH3+ (only use with zwitterions containing
> exactly one residue) but the result was the same)
>
> Screen-out:
> http://pastebin.com/CuMa7aZ7#
>
> topology:
> http://pastebin.com/FSbcFGYR
>
>

It appears that there are simply no parameters in the OPLS-AA force field for 
this entity.  Whether or not this is because OPLS-AA doesn't officially have 
parameters for it or they are just missing from the GROMACS implementation is 
something you'd have to dig into, but largely it seems that all dihedral 
parameters for the N- and C-terminal forms of PRO are all the same, so you can 
likely just use the same parameters in ffbonded.itp for this dihedral in the 
zwitterionic form.

-Justin

> Thanks in advance,
> Kevin
>
> On Tue, Jun 2, 2015 at 12:11 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 6/1/15 12:09 PM, Kevin C Chan wrote:
>>
>>> ​Thanks Justin,
>>>
>>> I did not but I tried just now. The aforementioned dihedral terms ​remain
>>> along with the errors.
>>>
>>>
>> Please provide your full pdb2gmx command, all screen output, and full
>> topology.  Use file sharing services, pastebin, etc. as needed.
>>
>> -Justin
>>
>>
>>   Thanks in advance,
>>> Kevin
>>>
>>> On Mon, Jun 1, 2015 at 11:13 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 6/1/15 10:57 AM, Kevin C Chan wrote:
>>>>
>>>>   Dear Users,
>>>>>
>>>>> I am testing with OPLSSaa force-field of proline. First I arbitrarily
>>>>> extract a single PRO from a pdb and fed into pdb2gmx. The resulted gro
>>>>> and
>>>>> top are however not suitable for further grompp (even minimization). The
>>>>> error messages are as follows:
>>>>>
>>>>> ERROR 1 [file topol.top, line 161]:
>>>>>      No default Ryckaert-Bell. types
>>>>>
>>>>> When I look into the line 161, it refers to a dihedral term concerning
>>>>> (CD
>>>>> N CA C) which is not able to be found in ffbonded.itp. However, other
>>>>> dihedral terms such as (CD N CA CB) or (CD N CA HA) which are also not
>>>>> found in itp do not report such error and I was successful to grompp
>>>>> after
>>>>> commenting out the line 161.
>>>>>
>>>>> Why would this happen?
>>>>>
>>>>>
>>>>>   Did you choose the proper "PRO-ZWITTERION-*" termini when running
>>>> pdb2gmx?
>>>>
>>>> -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
>>>>
>>>> ==================================================
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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

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