Sorry to take so long in replying--I'm not certain exactly what's wrong,
but one thing that may help is to insert the box size (I assume you are
using a water box) on the first line after the namelist amber input.
Here is a sample input file for a solvated protein:DNA complex in which
the system is heated from 5 to 300K over a 50-ps period using the NMR
ramping method (no NMR data are actually needed for this):
# PME-MD with belly: heating 50 ps, 5K to 300K
&cntrl
imin=0, ibelly=1, nmropt=1, iewald=1,
ntx=1, isolvp=1465,
ntpr=500, ntwx=500, ntwe=500,
ntwvm=0, ntwem=0, ntwxm=0,
ntf=2, idiel=1, dielc=1.0, cut=8.0,
nsnb=10, scnb=2.0, scee=1.2,
init=3, nrun=1050, nstlim=500, dt=0.002,
temp0=300.0, tempi=5.0, ntt=5, tautp=0.25, tauts=0.25,
taup=0.2, ntc=2, ntb=2, ntp=1,
&end
49.615436 37.000660 72.573906 90.0 90.0 90.0
50 36 72 4.0 0.0 0.0 0.0
0.00001
&wt
type='TEMP0', istep1=0, istep2=25000,
value1=5.0, value2=300.0,
&end
&wt
type='TEMP0', istep1=25001, istep2=525000,
value1=300.0, value2=300.0,
&end
&wt
type='END',
&end
&rst
IAT(1)=0,
&end
Restrain the terminal base pairs (i.e. all others in belly)
RES 1 61
RES 63 68
RES 71 76
RES 78 4629
END
END
This also carries out 1000 ps (1 ns) of production dynamics.
I hope this helps--please send e-mail again if you have any more
questions. Good luck!
Sincerely,
Michael Cooney
Dept. of Biochemistry and Molecular Biology
The University of Georgia
Athens, GA 30602, USA
On Thu, 30 Nov 2000, GIOVA wrote:
> I'm trying to start a dynnamic calculation from a minimization restart
> file using PME but the dynamic doesn't start and the .info file appears
> like that:
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 49.83 PRESS =
> 0.00
> Etot = nan EKtot = 3717.9879 EPtot = nan
> BOND = 7283.3858 ANGLE = 2961.6355 DIHED =
> 1531.1235
> 1-4 NB = 1093.7476 1-4 EEL = 12371.7763 VDWAALS =
> 26778.8005
> EELEC = nan EHBOND = 0.0000 CONSTRAINT =
> 0.0000
> T_SOLUTE = 49.1895 T_SOLVENT = 49.9763
> Ewald error estimate: nan
>
> My input is:
>
> #Sander input for Dymamic
> #
> &cntrl
> imin=0,nmrmax=0,
> ntx=1,irest=0,
> ntpr=100,ntwx=100,ntwv=0,ntwe=100,ntwxm=0,
> ntf=1,ntb=1,ntp=0,idiel=1,dielc=1.0,cut=10.0,
> nsnb=25,scnb=2.0,scee=1.2,
> nrun=40,nstlim=500,dt=0.001,ntcm=1,
> temp0=298.0,tempi=50.0,
> ig=71277,ntt=5,tautp=0.2,tauts=0.2,
> iewald=1,
> &end
> 80 80 72 90.0 90.0 90.0
> 80 80 72 3 0 0 0
> 0.00001
> END
> END
>
> And the sad end of the sandout is:
>
> bombs away
> bombs away
> bombs away
> bombs away
> bombs away
> bombs away
> bombs away
> bombs away
> bombs away
> BIG PROBLEM in grid_ucell!!!
>
> Can you please help me?
>
> TIA
>
> G.Bottegoni
>
> Dep. Ph. Sciences - University of Bologna - Italy
>
>
Received on Wed Jan 31 2001 - 13:13:47 PST
