[gmx-users] Distance Restraints Problem

[Gaurav Porwal]

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
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