[gmx-users] HELP:Fatal error: There were 1 error(s) processing your input

[Mark Abraham]

¹ù½¨Â· wrote:
>  Hi all:
> 
>   I want to start simulation of protein  that has heme group(FE).After learning the force field paremeter ,i add heme parameters to the force field's .rtp and .hdb file,and define a new bond  
> 
> . i operated the gromacs command as followed.
> 
> 1 pdb2gmx -ignh -ff G43a1 -f ffg43a1.pdb -o ffg43a1.pdb -p ffg43a1.top -water spce
> 
> 2 editconf -bt cubic -f ffg43a1.pdb -o ffg43a1_cub.pdb -d 0.9
> 
> 3 genbox -cp ffg43a1.pdb  -cs spc216.gro -o ffg43a1_box.gro -p ffg43a1.top
> 
> and then i edit a em.mdp file:
> 
> title = ga431
> cpp = /lib/cpp
> 
> define = -DFLEXIBLE
> 
> constraints = none
> 
> integrator = steep
> 
> dt = 0.002 ; ps !
> 
> nsteps = 10
> 
> nstlist = 5
> 
> ns_type = grid
> 
> rlist = 0.9
> 
> coulombtype = PME
> 
> rcoulomb = 0.9
> 
> vdwtype = cut-off
> 
> rvdw = 1.4
> 
> 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
> 
> the nsteps =10 because i just want to go through  it 
> 
> and then i run command grompp
> 
> 4 grompp -f em.mdp -c ffg43a1_box.gro -p ffg43a1.top -o ffg43a1.tpr
> 
> but a Fatal error emerged  : There were 1 error(s) processing your input, 
> i thought i made a wrong define of the heme residue,so i repeat the gromacs command using the protein without heme group.
> Unfortunately,the error comes again,with a difference of total charge (7.0 without heme,2.95 with heme)
> the error shows as followed:
> 
> 
> creating statusfile for 1 node...
> ' for variable optimize_fft, using 'no'
> Next time use one of: 'no' 'yes'

Probably you've broken your .mdp file somewhere, perhaps by editing it 
on a Windows machine. Use dos2unix to fix, in that case.

> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
> checking input for internal consistency...
> calling /lib/cpp...
> processing topology...
> Generated 279 of the 1225 non-bonded parameter combinations
> Excluding 3 bonded neighbours for Protein 1
> Excluding 2 bonded neighbours for SOL 27299
> NOTE:
>   System has non-zero total charge: 7.000003e+00
> 
> processing coordinates...
> double-checking input for internal consistency...
> 
> -------------------------------------------------------
> Program grompp, VERSION 3.3.3
> Source code file: grompp.c, line: 1132
> 
> Fatal error:
> There were 1 error(s) processing your input
> -------------------------------------------------------
>   Does anyone help me amd tell me how to hand this problem??? i will go crazy!

Yes... look back in the output for where it described the error, and fix 
it. Also, you should probably seriously consider upgrading to a newer 
and much faster GROMACS version, unless you need 3.3.3 for consistency 
with earlier work.

Mark