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

[Kevin C Chan]

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


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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