[AMBER] lipid simulation with Lipid14 FF failed

From: Albert <mailmd2011.gmail.com>
Date: Tue, 16 Aug 2016 12:00:50 +0200


I am trying to use Lipid 14 for protein-ligand membrane MD simulation. I
built the system from Charmm-gui and following steps:


The minimization steps finished without any problems and it generated a
mini.rst file successfully. However, my second step 02-heat failed with

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
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
   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
   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)
   ioutfm=1, ! Write a binary (netcdf) trajectory
   ntxo=2, ! Write binary restart files
   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

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


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Received on Tue Aug 16 2016 - 03:30:03 PDT
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