AMBER Archive (2006)

Subject: Re: AMBER: Problem with restarting MD simulation

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Tue Aug 08 2006 - 06:08:27 CDT

are you sure that file exists and is in the same directory?
type
 ls -la l42b18_eqm1.rst

Gobind Bisht wrote:

> 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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