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

[Kevin C Chan]

​Thanks Justin,

I did not but I tried just now. The aforementioned dihedral terms ​remain
along with the errors.

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