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

[Mijiddorj Batsaikhan]

Dear Justin,

Thank you very much.


Best regards,

Mijiddorj




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
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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>