Hello:
I am trying to use Lipid 14 for protein-ligand membrane MD simulation. I
built the system from Charmm-gui and following steps:
http://ambermd.org/tutorials/advanced/tutorial16/
The minimization steps finished without any problems and it generated a
mini.rst file successfully. However, my second step 02-heat failed with
messages:
lipid14> pmemd -O -p sys.prmtop -i 02-heat.in -o 02_heat.out -r
02-heat.rst -c 01-mini.rst -ref 01-mini.rst -x 02-heat.nc -inf
02-heat.infoforrtl: severe (24): end-of-file during read, unit 5, file
/home/albert/Documents/2016/0810/EP2-10024271A/lipid14/02-heat.in
Image PC Routine Line Source
libifcore.so.5 00002B5E02609998 Unknown Unknown Unknown
libifcore.so.5 00002B5E0264851E Unknown Unknown Unknown
Here is my 02-heat.in:
-----------------------------------------------------
Lipid heating 100K
&cntrl
imin=0, ! Molecular dynamics
ntx=1, ! Positions read formatted with no initial velocities
irest=0, ! No restart
ntc=2, ! SHAKE on for bonds with hydrogen
ntf=2, ! No force evaluation for bonds with hydrogen
tol=0.0000001, ! SHAKE tolerance
nstlim=250000, ! Number of MD steps
ntt=3, ! Langevin thermostat
gamma_ln=1.0, ! Collision frequency for Langevin thermostat
ntr=1, ! Restrain atoms using a harmonic potential
! (See the GROUP input below)
ig=-1, ! Random seed for Langevin thermostat
ntpr=100,
ntwr=10000,
ntwx=100, ! Write to trajectory file every ntwx steps
dt=0.001, ! Timestep (ps)
nmropt=1, ! NMR restraints will be read (See TEMP0 control below)
ntb=1,
ntp=0,
cut=10.0,
ioutfm=1, ! Write a binary (netcdf) trajectory
ntxo=2, ! Write binary restart files
/
&wt
type='TEMP0', ! Varies the target temperature TEMP0
istep1=0, ! Initial step
istep2=20000, ! Final step
value1=0.0, ! Initial temp0 (K)
value2=100.0 / ! final temp0 (K)
&wt type='END' / ! End of varying conditions
Hold lipid fixed
10.0 ! Force constant (kcal/(mol Angstroms^2))
RES 1 653 ! Choose residues
&END ! End GROUP input
&END
-----------------------------------------------------
The first residue in my system is the ligand, followed by protein and
lipids. There are 653 residues in all, excluding water and ions.
I am just wondering where is the problem?
Thanks a lot
Albert
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Received on Tue Aug 16 2016 - 03:30:03 PDT
