[gmx-users] Fatal error: Unknown bond_atomtype cn9 in Charmm27

[Justin Lemkul]

On 1/16/17 4:02 AM, Mijiddorj Batsaikhan wrote:
> Dear Justin,
>
> Thank you very much for quick response.
>
> I want to capitalize cn9, but I could not find small cn9 in my force field.
> There is CN9 (capital) only for DNA. There is not any DNA molecules in my
> system.
>

The error you posted before comes from a bonded interaction using cn9.  This 
means it's somewhere in ffnabonded.itp, probably in [dihedraltypes].  The fact 
that CN9 is used by DNA only does not depend on the contents of your system; the 
force field itself must be syntactically correct.

-Justin

>
> Best regards,
> Mijiddorj
>
>
>
> On 1/15/17 11:04 PM, Mijiddorj Batsaikhan wrote:
>> Dear gmx users,
>>
>> I am using gromacs-v5.1 with charmm27 force field that extended by
>> swissparams D amino acids.
>>
>> I got a following error.
>>
>> *************************************
>> Fatal error:
>> Unknown bond_atomtype cn9
>> *************************************
>> I searched some solutions, but there is no clear solution.
>> I also checked in atomtype.atp, etc., I could not find cn9, There are all
>> CN9.
>>
>> How can I fix this error? please advice me for modification of FF.
>>
>
> Capitalize it.  GROMACS atom types are case-sensitive.
>
> -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
>
> ==================================================
>

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

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

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