[gmx-users] mobile ligand with intermolecular interactions

[Ahmet Yildirim]

Dear users,

I add the following [ intermolecular_interactions ] section into the
topology file of protein-ligand complex for free energy calculations.
Unfortunately this setting doesn't provide me what I want in the decoupled
state. The ligand in the decoupled state is very mobile compared to the
coupled state. It means that the conformational sampling of the ligand in
the decoupled state is quite different from the coupled state. That is not
expected of course. Any suggestions as to why this might be?

Do you think that there is something wrong with the following settings,
e.g. [ dihedrals ] part?

[ intermolecular_interactions ]
[ bonds ]
; ai     aj    type   bA      kA     bB      kB
 1391    2615  6      0.654   0.0    0.654   4184.0

[ angles ]
; ai     aj    ak     type    thA      fcA        thB      fcB
 1393   1391   2615   1       88.8     0.0        88.8     41.84
 1391   2615   2614   1       32.9     0.0        32.9     41.84

[ dihedrals ]
; ai     aj    ak    al    type     thA      fcA       thB      fcB
 1410  1393  1391  2615    2       -159.7    0.0    -159.7    41.84
 1393  1391  2615  2614    2        122.6    0.0     122.6    41.84
 1391  2615  2614  2610    2         12.8    0.0      12.8    41.84


Should I use the following [ dihedral_restraints ] part instead of the
above [ dihedrals ] part?
[ dihedral_restraints ]
;   ai    aj    ak    al  type    phiA     dphiA  fcA    phiB      dphiB
fcB
 1410  1393  1391  2615     1    -159.7   0.0    0.0    -159.7    0.0
41.84
 1393  1391  2615  2614     1     122.6   0.0    0.0     122.6    0.0
41.84
 1393  1391  2615  2614     1      12.8   0.0    0.0     12.8     0.0
41.84

I think [ dihedral_restraints ] will be the same as [ dihedrals ] because
the eq. 4.84 in the manual will be equal to 4.61 if dphiA and dphiB are
taken as 0 (zero), right?


Thanks in advance

-- 
Ahmet Yildirim