[gmx-users] query respect to perl distances.pl

[Justin Lemkul]

On 5/11/13 12:38 AM, Arunima Shilpi wrote:
> Respected Sir
>
> Presently my work includes umbrella sampling for protein ligand
> interaction. The components of md_pull.mdp is
>
> title       = Umbrella pulling simulation
> define      = -DPOSRES_B
> ; Run parameters
> integrator  = md
> dt          = 0.002
> tinit       = 0
> nsteps      = 250000    ; 500 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            = umbrella
> pull_geometry   = distance  ; simple distance increase
> pull_dim        = N N Y
> pull_start      = yes       ; define initial COM distance > 0
> pull_ngroups    = 1
> pull_group0     = Protein
> pull_group1     = prc
> pull_rate1      = 0.01      ; 0.01 nm per ps = 10 nm per ns
> pull_k1         = 1000      ; kJ mol^-1 nm^-2
>
> where prc is my ligand. ...
>
> than I run
>
> trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep
>
> it generates 500 conf.gro files... but when i run the command
>
> perl distances.pl it gives following error
>
> atom number 2927 in an index group is larger than number of atoms in
> the trajectory (2836)
>
> which means the trajectory file does not include the ligand component
> how to overcome this error
>

You didn't say what groups you chose when you ran trjconv, but clearly the 
output group doesn't include the ligand.  Stick with the whole system; you need 
the full coordinates anyway to set up the umbrella sampling windows.

Note that position restraints are not normally necessary in these pulling 
simulations.  Given the nomenclature used, I suspect you're trying to rigidly 
adhere to the methodology of my tutorial, which represents a more specialized 
case.  Refer to our paper (as suggested by the tutorial) for why we used 
restraints.  For most protein-ligand interaction studies, restraints should not 
be necessary.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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