[gmx-users] binding free energy with gromacs2016

[Qasim Pars]

Dear users,

Hope someone will answer the questions in my previous mail.

Thanks in advance,

> On 6 Nov 2016, at 23:48, Qasim Pars <qasimpars at gmail.com> wrote:
> 
> Dear users,
> 
> I will try to do binding free energy calculation using GROMACS2016 but I am confused a little bit about the preparation of  the input files. I have a few questions:
> 
> 1) There are below lines to apply a harmonic distance restraint in the mdp files of the binding free energy tutorial http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme
> 
> pull           = umbrella 
> pull_geometry  = distance
> pull_dim       = Y Y Y
> pull_start     = no
> pull_init1     = 0.654
> pull_ngroups   = 1
> pull_group0    = a_1391
> pull_group1    = a_2615
> pull_k1        = 0.0   ; kJ*mol^(-1)*nm^(-2)
> pull_kB1       = 4184  ; kJ*mol^(-1)*nm^(-2)
> 
> Question 1: Instead of those lines I would like to use the [ intermolecular_interactions ] section in the topology file with GROMACS2016. Could you please tell me what to write the [ intermolecular_interactions ] section? 
> 
> 2) complex.top file of the tutorial is as follows:
> ; Include forcefield parameters
> #include "amber99sb-ildn.ff/forcefield.itp"
> 
> [ atomtypes ]
> ;name  bond_type          mass        charge  ptype   sigma      epsilon
> c3            c3          0.0000      0.0000  A   3.39967e-01  4.57730e-01
> dc3           c3          0.0000      0.0000  A   0.00000e+00  0.00000e+00
> ....
> 
> Question 2: Why all values (sigma and epsilon) of dc3 are zero? 
> 
> [ nonbond_params ]
> ; i  j    func  sigma           epsilon
> c3   c3    1     3.3996700e-01   4.5773000e-01
> dc3  dc3   1     3.3996700e-01   4.5773000e-01
> ....
> Question 3: Why all values of dc3 aren't zero? 
> 
> [ angle_restraints ]
> ; ai     aj    ak    al    type     thA      kA         multA      thB      kB         multB
>  1393   1391   2615  1391  1        88.8     0.00       1          88.8     41.84   1  
>  1391   2615   2614  2615  1        32.9     0.00       1          32.9     41.84   1         
> 
> [ dihedral_restraints ]
> ; ai    aj    ak    al       type   phiA     dphiA   kA          phiB     dphiB   kB
>   1410  1393  1391  2615     1      -159.7  0.0      0.00        -159.7   0.0     41.84
>   1393  1391  2615  2614     1      122.6   0.0      0.00         122.6   0.0     41.84
>   1391  2615  2614  2610     1      12.8    0.0      0.00          12.8   0.0     41.84
> .....
> Question 4: Do I still need to put those ligand parameters (dc3, [ angle_restraints ], [ dihedral_restraints ] ... ) into the topology file to use with GROMACS2016?
> 
> I read section 5.4.2 and 6.1 of the GROMACS2016 manual but I couldn't understand how to prepare the input files.
> -- 
> Qasim Pars