[gmx-users] nvt equilibration: error

[Justin Lemkul]

On 6/4/15 10:00 AM, marzieh dehghan wrote:
> 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
>

This is not so much a ligand as it is a custom residue; given that there is a 
covalent bond.  Following 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field 
will alleviate basically all of your issues.

>
>
> 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
>

You're merging a group with itself; this achieves nothing.

See the above link to a solution to your problem.

-Justin

> 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*
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================