[gmx-users] grompp does not find atomtype

[Justin Lemkul]

On 7/2/14, 9:31 AM, Dawid das wrote:
> Excuse me but I don't think we understand each other. If there are three
> atoms for instance and two of them are bonded and the third is not then how
> can I obtain or derive parameters for them? That is what I do not
> understand.
>

See my previous message.  The atoms you think aren't bonded actually are.

-Justin

>
>
> 2014-07-02 15:29 GMT+02:00 Dawid das <addiw7 at googlemail.com>:
>
>> Beside that, why do you say that 978-992 are bonded? According to visual
>> inspection of mCherry7-solv-ion.gro there is no connection between them (as
>> it should be) and also in mCherry7.top there is no bonding parameter for
>> them.
>>
>>
>> 2014-07-02 15:22 GMT+02:00 Dawid das <addiw7 at googlemail.com>:
>>
>>
>>> 2014-07-02 13:50 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>>>
>>> The problems almost certainly stem from the manipulations you've made to
>>>> the angles and dihedrals.  I don't understand why you've commented some of
>>>> them out.  For instance, the first angle that you've removed is atoms
>>>> 977-978-992, which clearly should have an angle interaction because 977-978
>>>> and 978-992 are bonded.  Simply removing "inconvenient" interactions (i.e.
>>>> lacking parameters or whatever) leads to a total meltdown of the model.
>>>
>>>
>>>
>>>
>>> Okey, but what should I do if there are missing parameters for
>>> combination of atoms which are not bonded?
>>> For instance: 973-977-978-992 atoms are not bonded but still in *top
>>> there is an "torsion interaction" for these atoms? What does it mean? It
>>> seems like some of the atom types are confused? Is it possible that I
>>> defined them in ambigous way?
>>>
>>
>>

-- 
==================================================

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

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