[gmx-users] umbrella sampling Protein_ligand complex distance calculation

[Justin Lemkul]

On 1/12/18 7:09 AM, rose rahmani wrote:
> 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!

It's not ridiculous, but there is logic in either approach. My preferred 
approach is to use trjconv -sep to quickly extract every frame, compile 
the distances of each with consistent labels (frame numbers, not time) 
and then you very easily (1) have the coordinate files already extracted 
and (2) you know exactly which frames to use by frame number.

Without using my approach, one can easily analyze the entire trajectory 
(perfectly fine) but then manually go back using trjconv -dump and 
specify the desired frames by time. I find this to be tedious and not 
easily automated.

-Justin

>
> 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.
>>
>>
>> Please help me to sort out this problem.
>>
>>
>>
>>
>>
>> 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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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================