Hi All,
I can't seem to figure this one out.
(note: running on centOS 6.4, Amber14/AmberTools14 with all bugfixes as of
7/20/2014, on Nvidia GeForce GTX 680)
I'm using similar inputs as the lipid tutorial (
http://ambermd.org/tutorials/advanced/tutorial16/) (with 2 proteins on the
membrane).
During the second step - 02_Heat.in
pmemd.cuda is giving me an error at the point where I am attempting to hold
the lipid fixed.
5. REFERENCE ATOM COORDINATES
default_name
----- READING GROUP 1; TITLE:
Hold lipid fixed
GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000
rfree: Error decoding variable 4 2 from:
RES 328 1161
The 02_heat.in looks like:
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=2500, ! Number of MD steps
ntt=3, ! Langevin dynamics
gamma_ln=1.0, ! Collision frequency for Langevin dynamics
ntr=1, ! Restrain atoms using a harmonic potential
! (See the GROUP input below)
ig=-1, ! Random seed for Langevin dynamics
ntpr=100,
ntwr=10000,
ntwx=100, ! Write to trajectory file every ntwx steps
dt=0.002, ! 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=2500, ! 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 328 1161 ! Choose residues
END
END ! End GROUP input
Using ambpdb and the min.rst file, the PDB has 2 proteins Residues (1-166
and 167-327) then the lipid membranes (328-1161) followed by ions and water.
Somewhere on the mailing list I saw that adding a &end fixed the issue, but
that didn't help here.
Any insight would be appreciated.
Thanks,
Jonathan
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Received on Sun Jul 20 2014 - 21:00:02 PDT
