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

郭建路 zimoguojianlu at 163.com
Sat Aug 8 09:09:35 CEST 2009

 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'

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
  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!

thanks very very very much!!! 

                                                                    yours: jianli guo

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