Hello,
I am running a membrane protein simulation in Amber. The input file was generated from CHAMM-GUI. However, the job failed in step 6.3 with the following information. I am just wondering
what's happening?
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme
= 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 71.665 Box Y = 71.665 Box Z = 88.027
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 72 NFFT2 = 72 NFFT3 = 96
Cutoff= 10.000 Tol =0.100E-04
Ewald Coefficient = 0.27511
Interpolation order = 4
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
----- READING GROUP 1; TITLE:
Protein posres
GROUP 1 HAS HARMONIC CONSTRAINTS 2.00000
GRP 1 RES 1 TO 288
Number of atoms in this group = 4588
----- READING GROUP 2; TITLE:
Membrane posres
GROUP 2 HAS HARMONIC CONSTRAINTS 0.50000
ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE
INCLUDED IN GROUP BELOW
GRAPH NAME = O3 SYMBOL = * TREE SYMBOL = * RESIDUE
TYPE = CHL1
GRAPH NAME = P SYMBOL = * TREE SYMBOL = * RESIDUE
TYPE = POPE
GRAPH NAME = P SYMBOL = * TREE SYMBOL = * RESIDUE
TYPE = POPC
GRP 2 RES 1 TO 8669
Number of atoms in this group = 126
----- END OF GROUP READ -----
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 5180.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
** No weight changes given **
RESTRAINTS:
No valid redirection requests found
** No restraint defined **
Done reading weight changes/NMR restraints
Number of triangulated 3-point waters found: 8725
Sum of charges from parm topology file = 0.00000000
Forcing neutrality...
| Dynamic Memory, Types Used:
| Reals 2112779
| Integers 3077203
| Nonbonded Pairs Initial Allocation: 14224189
| GPU memory information (estimate):
| KB of GPU memory in use: 318845
| KB of CPU memory in use: 68861
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
---------------------------------------------------
|---------------------------------------------------
| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.33
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.80
|---------------------------------------------------
EP4-10024271A/amber>
-----------------------------------------------here is step
6.3.mdin-------------------------------
A NPT simulation for common production-level simulations
&cntrl
imin=0, ! No minimization
irest=1, ! This IS a restart of an old MD simulation
ntx=5, ! So our inpcrd file has velocities
! Temperature control
ntt=3, ! Langevin dynamics
gamma_ln=1.0, ! Friction coefficient (ps^-1)
temp0=310, ! Target temperature
! Potential energy control
cut=10.0, ! nonbonded cutoff, in Angstroms
! MD settings
nstlim=5000000, ! 25K steps, 25 ps total
dt=0.001, ! time step (ps)
! SHAKE
ntc=2, ! Constrain bonds containing hydrogen
ntf=2, ! Do not calculate forces of bonds containing hydrogen
! Control how often information is printed
ntpr=1000, ! Print energies every 1000 steps
ntwx=1000, ! Print coordinates every 1000 steps to the trajectory
ntwr=10000, ! Print a restart file every 10K steps (can be less
frequent)
! ntwv=-1, ! Uncomment to also print velocities to trajectory
! ntwf=-1, ! Uncomment to also print forces to trajectory
ntxo=2, ! Write NetCDF format
ioutfm=1, ! Write NetCDF format (always do this!)
! Wrap coordinates when printing them to the same unit cell
iwrap=1,
! Constant pressure control. Note that ntp=3 requires barostat=1
barostat=1, ! Berendsen... change to 2 for MC barostat
ntp=3, ! 1=isotropic, 2=anisotropic, 3=semi-isotropic w/
surften
pres0=1.0, ! Target external pressure, in bar
taup=0.5, ! Berendsen coupling constant (ps)
! Constant surface tension (needed for semi-isotropic scaling).
Uncomment
! for this feature. csurften must be nonzero if ntp=3 above
csurften=3, ! Interfaces in 1=yz plane, 2=xz plane, 3=xy plane
gamma_ten=0.0, ! Surface tension (dyne/cm). 0 gives pure semi-iso
scaling
ninterface=2, ! Number of interfaces (2 for bilayer)
! Restraint options
ntr=1, ! Positional restraints for proteins, sugars,
ligands, and lipid head groups
nmropt=1, ! Dihedral restraints for sugars and lipids
! Set water atom/residue names for SETTLE recognition
watnam='TIP3', ! Water residues are named TIP3
owtnm='OH2', ! Water oxygens are named OH2
/
&wt
type='END'
/
Protein posres
2.5
RES 1 288
END
Membrane posres
1.0
FIND
O3 * * CHL1
P * * POPE
P * * POPC
SEARCH
RES 1 8669
END
END
DISANG=step6.3_equilibration.rest
LISTIN=POUT
LISTOUT=POUT
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Received on Sun Aug 14 2016 - 00:00:03 PDT
