[gmx-users] grompp does not find atomtype

[Justin Lemkul]

On 6/27/14, 8:02 AM, Dawid das wrote:
> So with what diagnostic shall I provide you with?
>

Design the smallest test case possible, ideally just a single residue that uses 
your atom types.  Verify that you get the same error.  Then post (ideally) the 
coordinates, topology, and any force field files (file sharing links; the list 
does not accept attachments), or at minimum, the bonded section of the .top that 
is problematic (using grompp -pp here can be very useful, as it will explicitly 
put in the parameters so we can see what is going on).

-Justin

>
> 2014-06-27 13:50 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>
>>
>>
>> On 6/27/14, 2:02 AM, Dawid das wrote:
>>
>>> 2014-06-27 1:54 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>>>
>>>   If the force field you're using uses U-B angles, you should stick to
>>>> that.
>>>>    If you don't need the cross-term, just specify ub0 and kub as zero,
>>>> while
>>>> leaving sensible values for theta0 and ktheta.
>>>>
>>>
>>>
>>>
>>>
>>> Well so I did and I still get this error...
>>>
>>>
>> Then the error is coming from somewhere else, perhaps directly in the .top
>> itself, but given that you've posted nothing diagnostic after having fixed
>> ffbonded.itp, there's nothing anyone can possibly suggest.
>>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> 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 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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