Dear amber users,
I am not able to restart my MD simulations. sander
is giving the following error:
Unit 30 Error on OPEN: l42b18_eqm1.rst
The rst file is attached and output file is :
-------------------------------------------------------
Amber 9 SANDER 2006
-------------------------------------------------------
| Run on 08/06/2006 at 11:25:51
[-O]verwriting output
File Assignments:
| MDIN: md_eqm.in
| MDOUT: md_eqm1.out
|INPCRD: l42b18_eqm1.rst
| PARM: l42b18.prmtop
|RESTRT: l42b18_eqb2.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
Eqm md simulation of L42B18 dna in saltconc 5mM
&cntrl
imin=0,
irest=1,
ntwr=100,
ntx=5,
ntpr=100,
ntwx=1000,
nstlim=50000,
dt=0.001,
cut=12,
ntb=0,
igb=1,saltcon=0.05,
ntt=3, gamma_ln=1.0,
tempi=300,
temp0=305,
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 08/01/06 Time = 03:12:54
NATOM = 2662 NTYPES = 15 NBONH = 946 MBONA = 1924
NTHETH = 2242 MTHETA = 2966 NPHIH = 4770 MPHIA = 5222
NHPARM = 0 NPARM = 0 NNB = 14824 NRES = 84
NBONA = 1924 NTHETA = 2966 NPHIA = 5222 NUMBND = 37
NUMANG = 76 NPTRA = 42 NATYP = 25 NPHB = 0
IFBOX = 0 NMXRS = 34 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are modified Bondi radii (mbondi)
| Memory Use Allocated
| Real 139379
| Hollerith 16058
| Integer 159145
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 1773 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 100, ntrx = 1, ntwr = 100
iwrap = 0, ntwx = 1000, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, ntb = 0, igb = 1, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
saltcon = 0.05000, offset = 0.09000, gbalpha= 1.00000
gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
rdt = 0.00000, rgbmax = 25.00000
alpb = 0
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 50000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00100, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = 71277
temp0 = 305.00000, tempi = 300.00000, gamma_ln= 1.00000
Unit 30 Error on OPEN: l42b18_eqm1.rst
----------------------------------------------------------------------------------------------------------------
Please help...
thanx in advance...
--
Gobind Singh Bisht
Department Of Biotechnology
IIT Kharagpur, Kharagpur-721302
West Bengal,
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Received on Wed Aug 09 2006 - 06:07:10 PDT
