[gmx-users] nvt equilibration: error

[marzieh dehghan]

Hi
Deat Justin



I formed a covalent bond according to the following steps:

1-      Covalent bond was formed between insulin and glucose by hyperchem

2-      Topology file was created using topolbuild



*PS:* I checked topology file, it showed all atoms i.e, protein and ligand
were called as UNK



3-      Energy minimization was done by gromacs

But when I used these command “grompp –f nvt.mdp -c em.gro -p topol.top –o
nvt.tpr

I confronted to the following error:

*Group Protein not found in index file.*

*Group names must match either [moleculetype] names*

*or custom index group names,in which case you*

*must supply an index file to the '-n' option of grompp.*



After holding these command, make_ndx –f em.gro –o index.ndx



The following pattern was appeared

*  0 System              : 13871 atoms*

*  1 Other               :   523 atoms*

*  2 UNK                 :   523 atoms*

*  3 CL                  :    10 atoms*

*  4 Water               : 13338 atoms*

*  5 SOL                 : 13338 atoms*

*  6 non-Water          :   533 atoms*

*  7 Ion                 :    10 atoms*

*  8 UNK                 :   523 atoms*

*  9 CL                  :    10 atoms*

* 10 Water_and_ions      : 13348 atoms*



 I selected

2 | 8      as protein and UNK

4 | 9      as water and CL



But the same error was appeared

Group Protein_UNK not found in index file.
Group names must match either [moleculetype] names
or custom index group names,in which case you
must supply an index file to the '-n' option of grompp



*NVT.mdp*

title       = Protein-ligand complex NVT equilibration

define      = -DPOSRES  ; position restrain the protein and ligand

; Run parameters

integrator  = md        ; leap-frog integrator

nsteps      = 50000     ; 2 * 50000 = 100 ps

dt          = 0.002     ; 2 fs

; Output control

nstxout     = 100       ; save coordinates every 0.2 ps

nstvout     = 100       ; save velocities every 0.2 ps

nstenergy   = 100       ; save energies every 0.2 ps

nstlog      = 100       ; update log file every 0.2 ps

energygrps  = Protein LIG

; Bond parameters

continuation    = no            ; first dynamics run

constraint_algorithm = lincs    ; holonomic constraints

constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
constrained

lincs_iter      = 1             ; accuracy of LINCS

lincs_order     = 4             ; also related to accuracy

; Neighborsearching

ns_type     = grid      ; search neighboring grid cells

nstlist     = 5         ; 10 fs

rlist       = 0.9       ; short-range neighborlist cutoff (in nm)

rcoulomb    = 0.9       ; short-range electrostatic cutoff (in nm)

rvdw        = 1.4       ; short-range van der Waals cutoff (in nm)

; Electrostatics

coulombtype     = PME       ; Particle Mesh Ewald for long-range
electrostatics

pme_order       = 4         ; cubic interpolation

fourierspacing  = 0.16      ; grid spacing for FFT

; Temperature coupling

tcoupl      = V-rescale                     ; modified Berendsen thermostat

tc-grps     = Protein_UNK CL_Water    ; two coupling groups - more accurate

tau_t       = 0.1   0.1                     ; time constant, in ps

ref_t       = 300   300                     ; reference temperature, one
for each group, in K

; Pressure coupling

pcoupl      = no        ; no pressure coupling in NVT

; Periodic boundary conditions

pbc         = xyz       ; 3-D PBC

; Dispersion correction

DispCorr    = EnerPres  ; account for cut-off vdW scheme

; Velocity generation

gen_vel     = yes       ; assign velocities from Maxwell distribution

gen_temp    = 300       ; temperature for Maxwell distribution

gen_seed    = -1        ; generate a random seed



* I am looking forward to getting your nice answer*

*thanks a lot*

-- 




*Marzieh DehghanPhD Candidate of BiochemistryInstitute of biochemistry and
Biophysics (IBB)University of Tehran, Tehran- Iran.*