[gmx-users] umbrella sampling Protein_ligand complex distance calculation

["Ashwini Londhe"]

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


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