[gmx-users] duplicate angle index- angle restraint

Sadaf Rani sadafrani6 at gmail.com
Sun Apr 12 13:12:43 CEST 2020


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.

Thanks in advance for your kind help.

Regards.

Sadaf


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