Moeed wrote:
I would be most thankful if you could help me warning 1, note 1 and thr
fatal error. I I read about -n option but I dont know where in command
line i have to include it. Thank you.
Index files are passed to Gromacs tools on the command line, just like all the
other options. There is no required order. I do not believe you need an index
file; your .mdp file is fundamentally flawed (see below).
As a preface, are we still dealing with your hexane system? I presume so from
the names on the grompp command, but it is always best to apprise us of what
you're doing rather than relying on us to keep track of everyone's problems.
grompp -f pr -c Hexane_b4pr.gro -r Hexane_b4pr.gro -p HexaneModified-Residuename.top
-o Hexane_pr >& output.grompp_pr
output file:
output.grompp_pr
*WARNING 1 [file pr.mdp, line unknown]:
Unknown or double left-hand 'warnings' in parameter file*
There is no such .mdp option.
checking input for internal consistency...
*NOTE 1 [file pr.mdp, line unknown]:
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale thermostat.*
There have been numerous list discussions about Berendsen, as well as a good
body of literature about this topic. For equilibration and initial relaxation,
Berendsen is probably fine, but if you need a rigorously-defined canonical
distribution of kinetic energies, Berendsen is not appropriate.
Opening library file /chem_soft/gromacs/share/
gromacs/top/ffoplsaa.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'HEX'
Seems to me like you only have hexane...
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
renumbering atomtypes...
converting bonded parameters...
NOTE 2 [file HexaneModified-Residuename.top, line unknown]:
The largest charge group contains 20 atoms.
Since atoms only see each other when the centers of geometry of the charge
groups they belong to are within the cut-off distance, too large charge
groups can lead to serious cut-off artifacts.
For efficiency and accuracy, charge group should consist of a few atoms.
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
You've been advised at least twice (if not three times) how to deal with this
note. If you want free help, you have to at least demonstrate that you're
willing to help yourself. Even if you plow through and manage to get grompp to
generate your .tpr file, the simulation that it specifies will be deeply flawed,
if not entirely invalid.
initialising group options...
processing index file...
Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat
-------------------------------------------------------
Program grompp, VERSION 4.0.7
Source code file: readir.c, line: 1007
*Fatal error:
Group protein not found in indexfile.
Maybe you have non-default goups in your mdp file, while not using the
'-n' option of grompp.
In that case use the '-n' option.
*
-------------------------------------------------------
pr.mdp file:*************************************************************
warnings = 10
cpp = /lib/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 500 ; total 1.0 ps.
nstcomm = 1
nstxout = 10
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tau_t = 0.1 0.1
tc-grps = protein sol
ref_t = 300 300
If your system has only hexane, why are you telling grompp that you have a
protein in water? I'm guessing you're copying this .mdp file from some
tutorial. Before blindly trying to push through, consider what you're doing and
read the manual.
-Justin
; Pressure coupling is not on
Pcoupl = no
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
--
========================================
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
========================================
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