[gmx-users] duplicate angle index- angle restraint

[Justin Lemkul]

On 4/12/20 7:12 AM, Sadaf Rani wrote:
> Dear Gromacs users
>
> I am putting some restraints on bonds angles and dihedrals during free
> energy calculations for which the topology file section is as below:-
> ; distance restraints
> [ bonds ]
> ;    i     j  type     r0A     r1A     r2A    fcA    r0B     r1B     r2B
>   fcB
>    7968   213    10     0.382  0.382    10.0   0.0    0.382   0.382   10.0
> 4184.000
>
> [ angle_restraints ]
> ;   ai    aj    ak    al  type    thA      fcA    multA  thB      fcB
>   multB
>    7959  7968   213  7968     1    89.40    0.0    1     89.40     41.840
>   1
>    213   7968  7922  7968     1    66.78    0.0    1     66.78     41.840
>   1
>
> [ dihedral_restraints ]
> ;   ai    aj    ak    al   type    phiA   dphiA  fcA    phiB      dphiB  fcB
>    7959  7968   213   218     1    174.86    0.0    0.0    174.86    0.0
>   41.840
>    7922  7968   213   211     1    149.95    0.0    0.0    149.95    0.0
>   41.840
>    7952  7968   213   211     1    167.76    0.0    0.0    167.76    0.0
>   41.840
>
> grompp gives me warning that I have duplicate angle index when I remove
> column 4 (al) in angle restraints I get following message:-
>
>
> ERROR 1 [file topol.top, line 76867]:
>    Incorrect number of parameters - found 5, expected 3 or 6 for Angle Rest.
>    (after the function type).
>
> Could you please correct me in fixing this section, I followed table 5.14
> of gromacs manual.

Three atoms make an angle. You're specifying four, which is incorrect.

-Justin

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Justin A. Lemkul, Ph.D.
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