[gmx-users] grompp not enough parameters

[Marlon Sidore]

Thanks a lot ... I feel really dumb here ~~

Marlon Sidore


PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France


2016-06-15 17:26 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 6/15/16 11:07 AM, Marlon Sidore wrote:
>
>> Hello,
>>
>> I'm trying to use the amber03 ff to simulate a protein with iron clusters.
>> I got the right parameters from a paper but then grompp tells me:
>> "ERROR 1 [file clusters_ffbonded.itp, line 53]:
>>   Not enough parameters
>>
>>
>> ERROR 2 [file clusters_ffbonded.itp, line 54]:
>>   Not enough parameters
>>
>>
>> ERROR 3 [file clusters_ffbonded.itp, line 55]:
>>   Not enough parameters
>>
>>
>> ERROR 4 [file clusters_ffbonded.itp, line 56]:
>>   Not enough parameters
>>
>>
>> ERROR 5 [file clusters_ffbonded.itp, line 57]:
>>   Not enough parameters"
>>
>> The thing is, line 53 to 57 from this file is the dihedrals for one of the
>> clusters:
>> "SEHS    FEHS    SH      CT   9   0.0     8,5772      3
>> FEHS    SEHS    FEHS    SH   9   180.0   16,15024    5
>> SEHS    FEHS    NA      CR   9   180.0   5,69024     3
>> SEHS    FEHS    NA      CC   9   0.0     5,69024     3
>> FEHS    SEHS    FEHS    NA   9   180.0   4,26768     5"
>>
>> I don't understand where there are missing parameters. Indeed, a classical
>> line from the dihedrals of ffbonded.itp has the same number of parameters,
>> for example:
>> " C   N   CT  C     9     180.0      1.44390     2  ; Amber03"
>>
>> Did any of you run into this before ?
>>
>>
> Your force constants have commas.  Use decimal points, otherwise they're
> not parsed correctly.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
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> School of Pharmacy
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> University of Maryland, Baltimore
> 20 Penn St.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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