[gmx-users] MD simulation error : rRNA simulaion

[Tasneem Kausar]

In energy group you have given Protein and non-Protein and you are not
simulating a protein but RNA.

On Fri, Oct 6, 2017 at 8:15 AM, Tasneem Kausar <tasneemkausar12 at gmail.com>
wrote:

> In energy group you have given Potein and non-Protein and you are not
> simulation a protein but RNA.
>
> On Fri, Oct 6, 2017 at 12:53 AM, Hemant Arya <arya.hemant2009 at gmail.com>
> wrote:
>
>> Dear gromacs,
>> Greetings
>> I am trying to run a NVT with the following command.
>>
>> My mdp file is below
>>
>> 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     = 500       ; save coordinates every 0.2 ps
>> nstvout     = 500       ; save velocities every 0.2 ps
>> nstenergy   = 500       ; save energies every 0.2 ps
>> nstlog      = 500       ; update log file every 0.2 ps
>> energygrps  = Protein Non-protein
>> ; 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
>> cutoff-scheme   = Verlet
>> ns_type     = grid      ; search neighboring grid cells
>> nstlist     = 10         ; 10 fs
>> *rcoulomb    = 1.0       ; 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 Non-Protein    ; 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
>>
>>
>>
>> Error :
>>
>> GROMACS:      gmx grompp, VERSION 5.1.4
>> Executable:   /home/amouda/Desktop/gromacs-5.1.4/build/bin/gmx
>> Data prefix:  /home/amouda/Desktop/gromacs-5.1.4 (source tree)
>> Command line:
>>   gmx grompp -f nvt.mdp -c em-steep.gro -p trp.top -o pr-nvt.tpr -n
>> index.ndx
>>
>> Ignoring obsolete mdp entry 'title'
>>
>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.17#
>>
>> *ERROR 1 [file nvt.mdp]:*
>> *  With Verlet lists rcoulomb!=rvdw is not supported*
>>
>> Setting the LD random seed to 2859163501
>> Generated 20503 of the 20503 non-bonded parameter combinations
>> Generating 1-4 interactions: fudge = 1
>> Generated 17396 of the 20503 1-4 parameter combinations
>> Excluding 3 bonded neighbours molecule type 'RNA_chain_1'
>> turning all bonds into constraints...
>> Excluding 2 bonded neighbours molecule type 'SOL'
>> turning all bonds into constraints...
>> Excluding 1 bonded neighbours molecule type 'NA'
>> turning all bonds into constraints...
>> Setting gen_seed to 1604041440
>> Velocities were taken from a Maxwell distribution at 300 K
>> Removing all charge groups because cutoff-scheme=Verlet
>>
>>
>> When i gave equal parameter to coulomb (1.4) and rvdw (1.4) then it shows
>> different error
>> like
>> "Fatal error:
>> Group Protein referenced in the .mdp file was not found in the 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."
>>
>>
>> Please help me to solve the problem.
>> Thanks
>> --
>> *Hemant Arya*
>> Research Scholar
>> UGC-RGNF
>> Centre for Bioinformatics,
>> School of Life Sciences,
>> Pondicherry University
>> Kalapet
>> Puducherry- 605014
>> INDIA
>> Contact No. +91 9597221248
>>                    +91 2930-244141
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>