Dear Sirs,I have a problem with running the short simulation with GROMACS. I have a structure for a small ligand (drg.pdb after cleaning with PRODRG). For this ligand I have run PRODRG in order to get drg.gro file and drg.itp topology file. I have edited the drg.top in order to include drg.itp as #include. My goal is to run simulation in vacuum (no water) - with only ligand (!). No protein also. I have tried to run it but I am getting error message. It seem that GROMACS does not read my topology file. What I am doing wrong ?
grompp -f em.mdp -c drg.gro -p drg.top -o drg.tpr
Results:
....
creating statusfile for 1 node...
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 1284 of the 1485 non-bonded parameter combinations
processing coordinates...
Fatal error: number of coordinates in coordinate file (drg.gro, 25)
does not match topology (drg.top, 0)
Regards
Dariusz
PRODRG COORDS
25
1MOL C15 1 0.005 1.276 1.490
1MOL C14 2 0.069 1.200 1.373
1MOL O13 3 0.103 1.067 1.417
1MOL C12 4 0.166 0.994 1.309
1MOL C11 5 0.211 0.854 1.356
1MOL N8 6 0.102 0.758 1.382
1MOL C9 7 0.036 0.780 1.512
1MOL S7 8 0.161 0.606 1.376
1MOL O3B 9 0.291 0.595 1.448
1MOL O4B 10 0.178 0.567 1.233
1MOL C6 11 0.048 0.497 1.450
1MOL S2 12 0.055 0.329 1.454
1MOL C3 13 -0.086 0.320 1.543
1MOL S1 14 -0.138 0.161 1.586
1MOL O1A 15 -0.035 0.112 1.682
1MOL O2A 16 -0.276 0.164 1.642
1MOL N21 17 -0.127 0.082 1.444
1MOL HAB 18 -0.151 -0.014 1.439
1MOL C4 19 -0.136 0.441 1.569
1MOL C5 20 -0.065 0.543 1.519
1MOL C10 21 -0.093 0.696 1.527
1MOL N16 22 -0.151 0.729 1.658
1MOL HAA 23 -0.106 0.813 1.689
1MOL C17 24 -0.294 0.760 1.645
1MOL C18 25 -0.353 0.787 1.783
[ moleculetype ]
;name nrexcl
MOL 3
;
;
; This file was generated by PRODRG version 040607.0508
; PRODRG written/copyrighted by Daan van Aalten
;
; Questions/comments to [EMAIL PROTECTED]
;
; When using this software in a publication, cite:
; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
; PRODRG - a tool for high-throughput crystallography
; of protein-ligand complexes.
; Acta Crystallogr. D60, in press.
;
;
[ atoms ]
; nr type resnr resid atom cgnr charge
1 CH3 1 MOL C15 1 0.018
2 CS2 1 MOL C14 1 0.210
3 OS 1 MOL O13 1 -0.188
4 CS2 1 MOL C12 1 0.209
5 CH2 1 MOL C11 1 0.055
6 NL 1 MOL N8 1 -0.280
7 CH2 1 MOL C9 1 0.056
8 S 1 MOL S7 1 2.175
9 OM 1 MOL O3B 1 -0.862
10 OM 1 MOL O4B 1 -0.862
11 CB 1 MOL C6 1 -0.028
12 S 1 MOL S2 1 0.327
13 CB 1 MOL C3 1 -0.028
14 S 1 MOL S1 1 2.175
15 OM 1 MOL O1A 1 -0.862
16 OM 1 MOL O2A 1 -0.862
17 N 1 MOL N21 1 -1.078
18 H 1 MOL HAB 1 -0.004
19 CR51 1 MOL C4 1 -0.049
20 CB 1 MOL C5 1 -0.028
21 CH1 1 MOL C10 1 0.118
22 NL 1 MOL N16 1 -0.280
23 H 1 MOL HAA 1 -0.005
24 CH2 1 MOL C17 1 0.055
25 CH3 1 MOL C18 1 0.018
[ bonds ]
;ai aj fu c0 c1
1 2 1 0.153 334720.0 0.153 334720.0 ; C15 C14
2 3 1 0.144 251040.0 0.144 251040.0 ; C14 O13
3 4 1 0.144 251040.0 0.144 251040.0 ; O13 C12
4 5 1 0.153 334720.0 0.153 334720.0 ; C12 C11
5 6 1 0.147 376560.0 0.147 376560.0 ; C11 N8
6 7 1 0.147 376560.0 0.147 376560.0 ; N8 C9
6 8 1 0.163 229631.7 0.163 229631.7 ; N8 S7
7 21 1 0.153 334720.0 0.153 334720.0 ; C9 C10
8 9 1 0.150 376560.0 0.150 376560.0 ; S7 O3B
8 10 1 0.150 376560.0 0.150 376560.0 ; S7 O4B
8 11 1 0.175 261918.4 0.175 261918.4 ; S7 C6
11 12 1 0.172 264983.0 0.172 264983.0 ; C6 S2
11 20 1 0.139 418400.0 0.139 418400.0 ; C6 C5
12 13 1 0.172 264983.0 0.172 264983.0 ; S2 C3
13 14 1 0.175 261918.4 0.175 261918.4 ; C3 S1
13 19 1 0.133 418400.0 0.133 418400.0 ; C3 C4
14 15 1 0.150 376560.0 0.150 376560.0 ; S1 O1A
14 16 1 0.150 376560.0 0.150 376560.0 ; S1 O2A
14 17 1 0.163 333868.6 0.163 333868.6 ; S1 N21
17 18 1 0.100 374468.0 0.100 374468.0 ; N21 HAB
19 20 1 0.133 418400.0 0.133 418400.0 ; C4 C5
20 21 1 0.153 334720.0 0.153 334720.0 ; C5 C10
21 22 1 0.147 376560.0 0.147 376560.0 ; C10 N16
22 23 1 0.100 374468.0 0.100 374468.0 ; N16 HAA
22 24 1 0.147 376560.0 0.147 376560.0 ; N16 C17
24 25 1 0.153 334720.0 0.153 334720.0 ; C17 C18
[ pairs ]
;ai aj fu c0 c1
1 4 1 ; C15 C12
2 5 1 ; C14 C11
3 6 1 ; O13 N8
4 7 1 ; C12 C9
4 8 1 ; C12 S7
5 9 1 ; C11 O3B
5 10 1 ; C11 O4B
5 11 1 ; C11 C6
5 21 1 ; C11 C10
6 12 1 ; N8 S2
6 20 1 ; N8 C5
6 22 1 ; N8 N16
7 9 1 ; C9 O3B
7 10 1 ; C9 O4B
7 11 1 ; C9 C6
7 19 1 ; C9 C4
7 23 1 ; C9 HAA
7 24 1 ; C9 C17
8 13 1 ; S7 C3
8 19 1 ; S7 C4
8 21 1 ; S7 C10
9 12 1 ; O3B S2
9 20 1 ; O3B C5
10 12 1 ; O4B S2
10 20 1 ; O4B C5
11 14 1 ; C6 S1
11 22 1 ; C6 N16
12 15 1 ; S2 O1A
12 16 1 ; S2 O2A
12 17 1 ; S2 N21
12 21 1 ; S2 C10
13 18 1 ; C3 HAB
13 21 1 ; C3 C10
14 20 1 ; S1 C5
15 18 1 ; O1A HAB
15 19 1 ; O1A C4
16 18 1 ; O2A HAB
16 19 1 ; O2A C4
17 19 1 ; N21 C4
19 22 1 ; C4 N16
20 23 1 ; C5 HAA
20 24 1 ; C5 C17
21 25 1 ; C10 C18
23 25 1 ; HAA C18
[ angles ]
;ai aj ak fu c0 c1
1 2 3 1 109.5 284.5 109.5 284.5 ; C15 C14 O13
2 3 4 1 109.5 334.7 109.5 334.7 ; C14 O13 C12
3 4 5 1 109.5 284.5 109.5 284.5 ; O13 C12 C11
4 5 6 1 109.5 460.2 109.5 460.2 ; C12 C11 N8
5 6 7 1 109.5 376.6 109.5 376.6 ; C11 N8 C9
5 6 8 1 109.5 376.6 109.5 376.6 ; C11 N8 S7
7 6 8 1 109.5 376.6 109.5 376.6 ; C9 N8 S7
6 7 21 1 109.5 460.2 109.5 460.2 ; N8 C9 C10
6 8 9 1 109.5 460.2 109.5 460.2 ; N8 S7 O3B
6 8 10 1 109.5 460.2 109.5 460.2 ; N8 S7 O4B
9 8 10 1 109.5 460.2 109.5 460.2 ; O3B S7 O4B
6 8 11 1 109.5 460.2 109.5 460.2 ; N8 S7 C6
9 8 11 1 109.5 460.2 109.5 460.2 ; O3B S7 C6
10 8 11 1 109.5 460.2 109.5 460.2 ; O4B S7 C6
8 11 12 1 132.0 418.4 132.0 418.4 ; S7 C6 S2
8 11 20 1 120.0 418.4 120.0 418.4 ; S7 C6 C5
12 11 20 1 108.0 418.4 108.0 418.4 ; S2 C6 C5
11 12 13 1 108.0 418.4 108.0 418.4 ; C6 S2 C3
12 13 14 1 120.0 418.4 120.0 418.4 ; S2 C3 S1
12 13 19 1 108.0 418.4 108.0 418.4 ; S2 C3 C4
14 13 19 1 120.0 418.4 120.0 418.4 ; S1 C3 C4
13 14 15 1 109.5 460.2 109.5 460.2 ; C3 S1 O1A
13 14 16 1 109.5 460.2 109.5 460.2 ; C3 S1 O2A
15 14 16 1 109.5 460.2 109.5 460.2 ; O1A S1 O2A
13 14 17 1 109.5 460.2 109.5 460.2 ; C3 S1 N21
15 14 17 1 109.5 460.2 109.5 460.2 ; O1A S1 N21
16 14 17 1 109.5 460.2 109.5 460.2 ; O2A S1 N21
14 17 18 1 120.0 418.4 120.0 418.4 ; S1 N21 HAB
13 19 20 1 108.0 418.4 108.0 418.4 ; C3 C4 C5
11 20 19 1 108.0 418.4 108.0 418.4 ; C6 C5 C4
11 20 21 1 120.0 418.4 120.0 418.4 ; C6 C5 C10
19 20 21 1 132.0 418.4 132.0 418.4 ; C4 C5 C10
7 21 20 1 109.5 460.2 109.5 460.2 ; C9 C10 C5
7 21 22 1 109.5 460.2 109.5 460.2 ; C9 C10 N16
20 21 22 1 109.5 460.2 109.5 460.2 ; C5 C10 N16
21 22 23 1 109.5 376.6 109.5 376.6 ; C10 N16 HAA
21 22 24 1 109.5 376.6 109.5 376.6 ; C10 N16 C17
23 22 24 1 109.5 376.6 109.5 376.6 ; HAA N16 C17
22 24 25 1 109.5 460.2 109.5 460.2 ; N16 C17 C18
[ dihedrals ]
;ai aj ak al fu c0 c1 m c0 c1 m
11 8 12 20 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C6 S7 S2 C5
13 12 14 19 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C3 S2 S1 C4
20 11 21 19 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C5 C6 C10 C4
6 5 7 8 2 35.3 836.8 0 35.3 836.8 0 ; IDI N8 C11 C9 S7
8 6 9 10 2 35.3 836.8 0 35.3 836.8 0 ; IDI S7 N8 O3B O4B
14 13 16 15 2 35.3 836.8 0 35.3 836.8 0 ; IDI S1 C3 O2A O1A
21 7 22 20 2 35.3 836.8 0 35.3 836.8 0 ; IDI C10 C9 N16 C5
22 21 24 23 2 35.3 836.8 0 35.3 836.8 0 ; IDI N16 C10 C17 HAA
11 12 13 19 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C6 S2 C3 C4
12 13 19 20 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI S2 C3 C4 C5
13 19 20 11 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C3 C4 C5 C6
19 20 11 12 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C4 C5 C6 S2
20 11 12 13 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C5 C6 S2 C3
1 2 3 4 1 0.0 3.8 3 0.0 3.8 3 ; DI C15 C14 O13 C12
5 4 3 2 1 0.0 3.8 3 0.0 3.8 3 ; DI C11 C12 O13 C14
3 4 5 6 1 0.0 5.9 3 0.0 5.9 3 ; DI O13 C12 C11 N8
4 5 6 8 1 0.0 3.8 3 0.0 3.8 3 ; DI C12 C11 N8 S7
21 7 6 5 1 0.0 3.8 3 0.0 3.8 3 ; DI C10 C9 N8 C11
5 6 8 11 1 0.0 1.3 3 0.0 1.3 3 ; DI C11 N8 S7 C6
6 7 21 22 1 0.0 5.9 3 0.0 5.9 3 ; DI N8 C9 C10 N16
6 8 11 20 1 0.0 2.9 3 0.0 2.9 3 ; DI N8 S7 C6 C5
12 13 14 17 1 0.0 2.9 3 0.0 2.9 3 ; DI S2 C3 S1 N21
13 14 17 18 1 180.0 16.7 2 180.0 16.7 2 ; DI C3 S1 N21 HAB
11 20 21 22 1 0.0 0.4 6 0.0 0.4 6 ; DI C6 C5 C10 N16
7 21 22 24 1 0.0 3.8 3 0.0 3.8 3 ; DI C9 C10 N16 C17
25 24 22 21 1 0.0 3.8 3 0.0 3.8 3 ; DI C18 C17 N16 C10
drg.mol
Description: MOL mdl chemical test
drg.pdb
Description: Protein Databank data
; Include forcefield parameters #include "ffgmx.itp" #include "drg.itp"
; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; ; cpp = /lib/cpp ; define = -DFLEX_SPC ; constraints = none ; integrator = steep ; nsteps = 100 ; ; Energy minimizing stuff ; ; emtol = 2000 ; emstep = 0.01 ; nstcomm = 1 ; ns_type = grid ; rlist = 1 ; rcoulomb = 1.0 ; rvdw = 1.0 ; Tcoupl = no ; Pcoupl = no ; gen_vel = no title = drg_trp cpp = /lib/cpp ; location of cpp on SGI define = -DFLEX_SPC ; Use Fergusonâs Flexible water model [4] constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 500 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME ; Use particle-mesh ewald rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ;; ;; Energy minimizing stuff ;; emtol = 1000.0 emstep = 0.01
; ; File 'mdout.mdp' was generated ; By user: darman (1001) ; On host: linux ; At date: Thu Mar 2 12:58:07 2006 ; ; VARIOUS PREPROCESSING OPTIONS title = drg_trp cpp = /lib/cpp include = define = -DFLEX_SPC ; RUN CONTROL PARAMETERS integrator = steep ; Start time and timestep in ps tinit = 0 dt = 0.002 nsteps = 500 ; For exact run continuation or redoing part of a run init_step = 0 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps = ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed bd-temp = 300 bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol = 1000.0 emstep = 0.01 ; Max number of iterations in relax_shells niter = 20 ; Step size (1/ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr = 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 100 nstvout = 100 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint = 1000 ; Output frequency for energies to log file and energy file nstlog = 100 nstenergy = 100 ; Output frequency and precision for xtc file nstxtcout = 0 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist = 0.9 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-5 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = No ; Groups to couple separately tc-grps = ; Time constant (ps) and reference temperature (K) tau-t = ref-t = ; Pressure coupling Pcoupl = No Pcoupltype = Isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p = 1 compressibility = ref-p = ; Random seed for Andersen thermostat andersen_seed = 815131 ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing = ; Number of time points to use for specifying annealing in each group annealing_npoints = ; List of times at the annealing points for each group annealing_time = ; Temp. at each annealing point, for each group. annealing_temp = ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = no gen-temp = 300 gen-seed = 173529 ; OPTIONS FOR BONDS constraints = none ; Type of constraint algorithm constraint-algorithm = Lincs ; Do not constrain the start configuration unconstrained-start = no ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR = no ; Relative tolerance of shake shake-tol = 1e-04 ; Highest order in the expansion of the constraint coupling matrix lincs-order = 4 ; Number of iterations in the final step of LINCS. 1 is fine for ; normal simulations, but use 2 to conserve energy in NVE runs. ; For energy minimization with constraints it should be 4 to 8. lincs-iter = 1 ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than lincs-warnangle = 30 ; Convert harmonic bonds to morse potentials morse = no ; ENERGY GROUP EXCLUSIONS ; Pairs of energy groups for which all non-bonded interactions are excluded energygrp_excl = ; NMR refinement stuff ; Distance restraints type: No, Simple or Ensemble disre = No ; Force weighting of pairs in one distance restraint: Conservative or Equal disre-weighting = Conservative ; Use sqrt of the time averaged times the instantaneous violation disre-mixed = no disre-fc = 1000 disre-tau = 0 ; Output frequency for pair distances to energy file nstdisreout = 100 ; Orientation restraints: No or Yes orire = no ; Orientation restraints force constant and tau for time averaging orire-fc = 0 orire-tau = 0 orire-fitgrp = ; Output frequency for trace(SD) to energy file nstorireout = 100 ; Dihedral angle restraints: No, Simple or Ensemble dihre = No dihre-fc = 1000 dihre-tau = 0 ; Output frequency for dihedral values to energy file nstdihreout = 100 ; Free energy control stuff free-energy = no init-lambda = 0 delta-lambda = 0 sc-alpha = 0 sc-sigma = 0.3 ; Non-equilibrium MD stuff acc-grps = accelerate = freezegrps = freezedim = cos-acceleration = 0 ; Electric fields ; Format is number of terms (int) and for all terms an amplitude (real) ; and a phase angle (real) E-x = E-xt = E-y = E-yt = E-z = E-zt = ; User defined thingies user1-grps = user2-grps = userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0
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