[gmx-users] Distance Restraints Problem
David van der Spoel
spoel at xray.bmc.uu.se
Thu Aug 19 13:22:03 CEST 2004
On Thu, 2004-08-19 at 11:28, Gaurav Porwal wrote:
> Dear Gromacs Users,
>
> I'm using distance restraints to bring two beta strands close to form a
> beta sheet. I'm writing all the restraints in a file "disres.itp" and then
> including the file in the topology file. Also required definitions using
> "DEFINE" are provided in the mdp files (first one to minimize the energy
> "vac.mdp" and second to do the MD "md.mdp").
>
> When I run the minimization or the md step, following error is
> encountered:
>
> In file included from t.top:5633:
> disres.itp:3:37: missing terminating ' character
> cpp exit code: 256
> Tried to execute: '/lib/cpp -I/usr/local/share/gromacs/top -DDISRES t.top
> > gromppqtImAD'
> The '/lib/cpp' command is defined in the .mdp file
> processing topology...
> Generated 135 of the 1081 non-bonded parameter combinations
> Cleaning up temporary file gromppqtImAD
> Fatal error: [ file "disres.itp", line 4 ]:
> Atom index (14) in distance_restraints out of bounds (1-3)
>
> I even tried to remove this particular restraint but it shows the same
> behaviour for all the restraints.
>
> Can anybody tell me what is the possible reason for this error.
>
> I'm attaching the restraint and mdp files for better reference.
> Kindly help me.
>
> PS - All simulations are being done in vacuum. All restraints are defined
> for C alpha atoms of various residues.
>
> Thank you.
>
> Regards,
> Gaurav
>
> --------------------------------------------------------------
> Distance restraint file
>
> [ distance_restraints ]
>
> ;ai aj type index type' low up1 up2 fac
You need to remove the apostrophe sign ' from the above line
> 14 326 1 1 1 0.0 0.4 0.6 2.0
> 26 338 1 2 1 0.0 0.47 0.53 2.0
> 35 356 1 3 1 0.0 0.47 0.53 2.0
> 43 368 1 4 1 0.0 0.47 0.53 2.0
> 52 386 1 5 1 0.0 0.47 0.53 2.0
> 69 394 1 6 1 0.0 0.47 0.53 2.0
> 26 657 1 7 1 0.0 0.42 0.46 2.0
> 35 640 1 8 1 0.0 0.48 0.52 2.0
> 43 631 1 9 1 0.0 0.42 0.46 2.0
> 52 619 1 10 1 0.0 0.48 0.52 2.0
> 631 710 1 11 1 0.0 0.48 0.52 2.0
> 640 698 1 12 1 0.0 0.42 0.46 2.0
> 657 686 1 13 1 0.0 0.48 0.52 2.0
>
>
> ----------------------------------------------------------------
> vac.mdp - energy minimzation file
>
> ;
> ; Input file
> ;
> title = Octamer ; a string
> cpp = /lib/cpp ; c-preprocessor
> dt = 0.002 ; time step
> define = -DDISRES
> ;define = -DFLEX_SPC
> integrator = steep
> tinit = 0.0
> nsteps = 500000 ; number of steps
> nstcomm = 1 ; reset c.o.m. motion
> nstxout = 2500 ; write coords
> nstvout = 5000 ; write velocities
> nstfout = 0
> nstlog = 5000 ; print to logfile
> nstenergy = 500 ; print energies
> nstlist = 10 ; update pairlist
> emtol = 20
> emstep = 0.01
>
> ; Neighbour Searching
> ns_type = simple ; pairlist method
> epsilon_r = 4
> ; Electrostatics and VdW
> coulombtype = shift
> vdwtype = shift
> rlist = 1.4 ; cut-off for ns
> rvdw_switch = 0.8
> rvdw = 1.4 ; cut-off for vdw
> rcoulomb_switch = 0.8
> rcoulomb = 1.4 ; cut-off for coulomb
> ;Temperature coupling
> Tcoupl = yes ; temperature bath
> (yes,no)
> ref_t = 298
> tc-grps = System
> tau_t = 0.1
> ; Pressure coupling
> Pcoupl = no ; pressure bath
> tau_p = 0.5
> compressibility = 4.575e-4
> ref_p = 1.0
> ; Velocity generation
> gen_vel = yes ; generate initial
> gen_temp = 298.0 ; initial temperature
> gen_seed = 173529 ; random seed
> constraints = none
> constraint_algorithm = shake
> shake_tol = 0.0001
> ; Distance restraints
> ;disre = simple
>
> --------------------------------------------------------------------
> md.mdp - MD file
>
> ;
> ; Input file
> ;
> title = Octamer ; a string
> cpp = /lib/cpp ; c-preprocessor
> dt = 0.002 ; time step
> define = -DDISRES
> integrator = md
> tinit = 0.0
> nsteps = 5000000 ; number of steps
> nstcomm = 1 ; reset c.o.m. motion
> nstxout = 2500 ; write coords
> nstvout = 5000 ; write velocities
> nstfout = 0
> nstlog = 5000 ; print to logfile
> nstenergy = 500 ; print energies
> nstlist = 10 ; update pairlist
> ; Neighbour Searching
> ns_type = simple ; pairlist method
> epsilon_r = 4
> ; Electrostatics and VdW
> coulombtype = shift
> vdwtype = shift
> rlist = 1.4 ; cut-off for ns
> rvdw_switch = 0.8
> rvdw = 1.4 ; cut-off for vdw
> rcoulomb_switch = 0.8
> rcoulomb = 1.4 ; cut-off for coulomb
> ;Temperature coupling
> Tcoupl = yes ; temperature bath
> (yes,no)
> ref_t = 298
> tc-grps = System
> tau_t = 0.1
> ; Pressure coupling
> Pcoupl = no ; pressure bath
> tau_p = 0.5
> compressibility = 4.575e-4
> ref_p = 1.0
> ; Velocity generation
> gen_vel = yes ; generate initial
> gen_temp = 298.0 ; initial temperature
> gen_seed = 173529 ; random seed
> constraints = all-bonds
> constraint_algorithm = shake
> shake_tol = 0.0001
> ; Distance restraints
> disre = simple
>
>
>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4205 fax: +46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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