[gmx-users] grompp does not find atomtype

[Dawid das]

O'right, I'ill do that but I have also noticed visually something strange.
The thing is that for my new residue there is no bond shown between two
atoms although the distance between them is correct and usual for C-S
single bond.
I used vmd and opened *.gro file. May that be a problem?


2014-06-28 13:56 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> 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
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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
>
> ==================================================
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> Gromacs Users mailing list
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