[gmx-users] grompp not enough parameters

[Justin Lemkul]

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

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

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