[gmx-users] grompp errors

[Justin A. Lemkul]

Please use an informative subject.

ITHAYARAJA wrote:
> Dear Sir,
> 
> when i am doing energy minimization (grompp), i found following error
> 
> CMD : grompp -f em.mdp -c proteinGR_b4ion.gro -p proteinGR.top -o 
> proteinGR_b4ion.tpr
> 
> WARNING 1 [file em.mdp, line unknown]:
>   Unknown or double left-hand 'coulomtype' in parameter file
> 

This error arises from a typo.

> 
> checking input for internal consistency...
> processing topology...
> Opening library file /usr/share/gromacs/top/ffgmx.itp
> Opening library file /usr/share/gromacs/top/ffgmxnb.itp
> Opening library file /usr/share/gromacs/top/ffgmxbon.itp
> Opening library file /usr/share/gromacs/top/ff_dum.itp
> Generated 1284 of the 1485 non-bonded parameter combinations
> 
> -------------------------------------------------------
> Program grompp, VERSION 4.0.7
> Source code file: ../../../../src/kernel/toppush.c, line: 947
> 
> Fatal error:
> Atomtype NR not found
> -------------------------------------------------------
> 

This error comes from the fact that you've tried to use a nonexistent atom type 
somewhere in the topology.  NR is a Gromos96 atom type, so whatever you're doing 
is likely mixing and matching force fields, which is inappropriate.

-Justin

> The parameter file contains,
> 
> title     =  GR-substrate
> cpp                 =  cpp
> define              =  -DFLEX_SPC
> constraints         =  none
> integrator          =  steep
> dt                  =  0.002    ; ps !
> nsteps              =  100
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> coulomtype        =  PME ; Use particle-mesh ewald
> rcoulomb            =  1.0
> 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
> 
> I could not understand what i did mistake, and where the problem was?
> 
> PLease help me to solve this error
> 
> 
> Thank you
> 

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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