# [gmx-users] umbrella sampling Protein_ligand complex distance calculation

rose rahmani rose.rhmn93 at gmail.com
Fri Jan 12 13:09:42 CET 2018

```I had this problem but i couldn't solve it.
But i can tell you just a temporary solution; Don't use -sep with
trjconv,then use the output conf as an input for gmx distance. it probably
gives you sth like this;

time                   distances
0.0000000    1.7537287    0.0238601    0.0428935   -1.7530417
2.0000000    1.7294775   -0.0426260   -0.0664551   -1.7276745
4.0000000    1.7153677    0.0664165    0.0698769   -1.7126565
.
.
.
.
just consider that time=2 >>> is 1 ps                     ( depends on dt )
=4  >>> is  2ps
= 6  >>> is  3ps .........
but distances are exactly the same.
Sorrry, i know maybe Dr.justin and all professionals don't agree with these
solutions, but i can understand,when you don't get a proper answer,
sometimes you have to ridiculous solutions.That's it!

On Fri, Jan 12, 2018 at 10:44 AM, "Ashwini Londhe" <615502 at kist.re.kr>
wrote:

>
>
>
> Hi
>
>
> Initially I followed US-gromacs tuitorial of Dr. Lemkul.it works very
> fine. so I following the same tutorial for ligand-protein complex.
>
>
> I have pulled the ligand over 300ps using following MD_pull.mdp and also
> generated  series of cordinate files (conf0.gro-conf300.gro) but problem is
> at distance calculation.
>
>
>
>
>
> title = Umbrella pulling simulation
>
>
> define = -DPOSRES
>
> ; Run parameters
>
> integrator = md
>
> dt = 0.002
>
> tinit = 0
>
> nsteps = 150000 ; 300 ps
>
>
> nstcomm = 10
>
> ; Output parameters
>
> nstxout = 5000 ; every 10 ps
>
> nstvout = 5000
>
> nstfout = 500
>
> nstxtcout = 500 ; every 1 ps
>
> nstenergy = 500
>
> ; Bond parameters
>
> constraint_algorithm = lincs
>
>
> constraints = all-bonds
>
> continuation = yes ; continuing from NPT
>
> ; Single-range cutoff scheme
>
> nstlist = 5
>
> ns_type = grid
>
> rlist = 1.4
>
> rcoulomb = 1.4
>
> rvdw = 1.4
>
> ; PME electrostatics parameters
>
> coulombtype = PME
>
> fourierspacing = 0.12
>
> fourier_nx = 0
>
> fourier_ny = 0
>
> fourier_nz = 0
>
> pme_order = 4
>
> ewald_rtol = 1e-5
>
> optimize_fft = yes
>
>
> ; Berendsen temperature coupling is on in two groups
>
> Tcoupl = Nose-Hoover
>
> tc_grps = Protein Non-Protein
>
> tau_t = 0.5 0.5
>
> ref_t = 310 310
>
> ; Pressure coupling is on
>
> Pcoupl = Parrinello-Rahman
>
> pcoupltype = isotropic
>
> tau_p = 1.0
>
> compressibility = 4.5e-5
>
> ref_p = 1.0
>
> refcoord_scaling = com
>
> ; Generate velocities is off
>
> gen_vel = no
>
> ; Periodic boundary conditions are on in all directions
>
> pbc = xyz
>
> ; Long-range dispersion correction
>
> DispCorr = EnerPres
>
> ; Pull code
>
> pull = yes
>
> pull_ngroups = 2
>
> pull_ncoords = 1
>
>
> pull_group1_name = Protein
>
>
> pull_group2_name = L6I
>
>
> pull_coord1_type = umbrella ; harmonic biasing force
>
>
> pull_coord1_geometry = distance ; simple distance increase
>
>
> pull_coord1_groups = 1 2
>
>
> pull_coord1_dim = N N Y
>
>
> pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
>
>
> pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
>
>
> pull_coord1_start = yes ; define initial COM distance > 0
>
>
>
>
>
> I have used distances.pl file from gromacs tutorial and change the group
> name Chain_A and Chain_B with L6I and Protein. Also replaced 500 frames
> with 300 frames. It generated summary_distance.dat file which does not
> include distances values.
>
>
>  After running script it generates this at the end
>
>
> .
>
>
> .
>
>
> .
>
>
> Processing configuration 300...
>
>
> readline () on closed filehandle IN at distances.pl line 16.
>
>
> Use of uninitializd value \$distance in concatenaton (.) or string at
> distans.pl line 30
>
>
>
>
>
> How could it happen by just changing Chain_A to L6I and Chain_B to Protein
> and conformations 500 to 300 it seems script works fine for peptide system
> only and not for protein_ligand complex.
>
>
>
>
>
> Also above error generated for ony proein-ligand complex and not for the
> peptide tutoral.
>
>
>
>
>
>
>
> Regards
>
>
> Ashwini Londhe
>
>
>
> Korea Institute of Science and Technology (KIST)
> 5, Hwarang-ro 14-gil
> Seongbuk-gu
> Seoul, 02792
> Republic of Korea
>
>
> (우: 02792) 서울특별시 성북구 화랑로 14길 5
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```