[gmx-users] Pro-lig under one molecule type

[Sana Saeed]

hi i am working of protein ligand binding free energy calculation, i have seen some tutorials, like from alchemistry websites and from some paper works. i made ligand topology with acpype (amber.ff) and used pdb2gmx for protein topology, then i combined gro files to make a complex. now i dont know how to make complex topology. i already studies and used tutorials from Bevanlab but it doesnt provide info about how to include protein and ligand as one moleculetype. and also how should i get the dihedral, angle and distance restraints. i studied gromacs manual about this but it doesnt provide any direction. if anyone have some tutorial, kindly suggest. Thanks in advance

 ; distance restraints[ bonds ];    i     j  type     r0A     r1A     r2A    fcA    r0B     r1B     r2B    fcB  2143  1656    10     0.615   0.615   10.0   0.0    0.615   0.615   10.0   4184.000
[ angle_restraints ];   ai    aj    ak    al  type    thA      fcA    multA  thB      fcB    multB  1658  1656  2143  1656     1    92.14    0.0    1    92.14    41.840    1  1656  2143  2142  2143     1    107.4    0.0    1    107.4    41.840    1 [ dihedral_restraints ];   ai    aj    ak    al  type    phiA     dphiA  fcA    phiB      dphiB  fcB  1668  1658  1656  2143     1    157.05   0.0    0.0    157.05    0.0    41.840  1658  1656  2143  2142     1    -129.56   0.0    0.0    -129.56    0.0    41.840  1656  2143  2142  2140     1    166.61   0.0    0.0    166.61    0.0    41.840




Sana Saeed Khan,Teaching-Research AssistantChemoinformatics LabGraduate Student, MS bioinfoDepartment of BioinformaticsSoongsil University, Seoul, South Korea.