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

[Justin Lemkul]

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

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