Dear Amber users,
I changed a bit my input file: see below
Heating
&cntrl
imin = 0,
irest = 0,
ntx = 1,
cut = 9,
ntb = 1,
iwrap = 1,
nmropt = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 200, dt = 0.002,
ntpr = 10, ntwx = 10, ntwr = 10,
/
&wt TYPE='END'
/
DISANG=dist.RST
LISTOUT=POUT
DUMPAVE=DISTout.RST.4
/
&end
my dist.RST
&rst iat=3457,4153
r1=0,r2=13.8,r3=13.8,r4=100.0,rk2=10.0,rk3=10.0, /
&end
The caclulations run but my DISTout.RST.4 is empty. What is wrong?
In out file I have:
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
** No weight changes given **
RESTRAINTS:
Requested file redirections:
DISANG = dist.RST
LISTOUT = POUT
DUMPAVE = DISTout.RST.4
Restraints will be read from file: dist.RST
Here are comments from the DISANG input file:
Number of restraints read = 1
Done reading weight changes/NMR restraints
Number of triangulated 3-point waters found: 24092
Sum of charges from parm topology file = 0.00000017
Forcing neutrality...
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 158552.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 158552. NUM_NOSHAKE = 0 CORRECTED RNDFP = 158552.
| TOTAL # of degrees of freedom (RNDF) = 158552.
---------------------------------------------------
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
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 19312266
| TOTAL SIZE OF NONBOND LIST = 19312266
Please guide me.
Urszula
> On Tue, Apr 08, 2014, Urszula Uciechowska wrote:
>>
>> Flags:
>> getting new box info from bottom of inpcrd
>> | INFO: Old style inpcrd file read
>>
>> | peek_ewald_inpcrd: Box info found
>> |Largest sphere to fit in unit cell has radius = 42.653
>
> This is OK. Something bad happened later. Usual advice: set ntpr=1 and
> nstlim=20. See if you get more information that will help resolve the
> problem.
>
> ....dac
>
>
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Received on Wed Apr 09 2014 - 00:30:02 PDT
