[gmx-users] Unknown bond_atomtype CAY

[Sameer Edirisinghe]

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 ?

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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