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
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!
thanks very very very much!!!
yours:
jianli guo
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