[gmx-users] Unknown bond_atomtype CAY

[Justin Lemkul]

On 10/8/16 2:58 AM, Sameer Edirisinghe wrote:
> Dear gromacs users, Dr. Justin,
>
> I managed to run md simulation with the aid of your helps here . As the
> next step I'm trying to create a crystal from polymer molecule so i can put
> several molecules to the same box and do a simulation. What approach should
> I take here ?
>

gmx genconf, gmx insert-molecules, etc.  See the manual.

If you're going to start doing something different, please start a new thread 
rather than dig up an old one that's not really related.

-Justin

> Regards
> Sameera Edirisinghe
>
> On Sep 22, 2016 00:41, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 9/21/16 7:42 AM, Sameer Edirisinghe wrote:
>>
>>> Dear Dr. Justin,
>>>
>>> Thanks for the explanation. Now i got the point you mentioned here. Then i
>>> checked the bonds i have mentioned in .rtp file and then i found the
>>> relevant bonded type. then i checked the ffbonded.itp file and i found
>>> that
>>> bond type is already in there.
>>> As an example,
>>>
>>> CAY  HA1 ; this is one of bond i have in .rtp file. and for that bond,
>>> relevant bond type (mentioned as below) was already in ffbonded.itp file
>>> CT    HC      1    0.10900   284512.0
>>>
>>> But still following error is occurring while running grompp.
>>>
>>> 1) ERROR 1 [file topol.top, line 108]:
>>>   No default Bond types
>>>
>>> 2) ERROR 2 [file topol.top, line 168]:
>>>   No default Angle types
>>>
>>> 3) ERROR 3 [file topol.top, line 426]:
>>>   No default Ryckaert-Bell. types
>>>
>>> How do i refer particular bond types in ffbonded.itp file to my current
>>> .gro file or any other relevant file ?
>>>
>>>
>> grompp won't complain about parameters being missing if they're actually
>> there. You're probably looking at the wrong line.
>>
>> -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

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