in cases like this it can be helpful to compare your mdin file with
one of the ones that you know worked properly in the test cases when
you ran them. if the overall format looks right, delete things 1 line
at a time until you find the problem one, then narrow down to the
specific variable.
one thing to check is the space in column 1- i don't use a space there
in my inputs.
On Wed, Jan 20, 2010 at 11:34 AM, MASLYK, MACIEJ MARCIN
<maciejmarcin.maslyk.ceu.es> wrote:
> Hi to everyone!
> I'm using Amber 10 to run MD simulation but after running the script I obtain error in all output files (for equilibration, minimization, dynamics). There is first column free in the input and I don't know where is the problem.
> Below is one of the outputs. Thank you for your suggestions.
>
> regards
>
> Maciek
>
> | Run on 01/20/2010 at 16:09:12
> [-O]verwriting output
> File Assignments:
> | MDIN: PYRc_md.in
> | MDOUT: PYRc_md.outmd
> |INPCRD: PYRc.rst
> | PARM: PYRc.tpp
> |RESTRT: PYRc_md.rsmd
> | REFC: PYRc.rst
> | MDVEL: mdvel
> | MDEN: mden
> | MDCRD: PYRc_md.coord
> |MDINFO: mdinfo
> |INPDIP: inpdip
> |RSTDIP: rstdip
>
> Here is the input file:
>
> Dinamica manteniendo fijo el soluto(25 ps)
> &cntrl
> nmropt = 1, ntx = 1, irest = 0, ntrx = 1,
> ntxo = 1,
> ntpr = 1000, ntwx =1000,
> ntf = 2, ntb = 2, dielc = 1.0,
> cut = 9., nsnb = 10, scnb = 2.0, scee = 1.2,
> ntr = 1, imin = 0, restraint_wt=50.0, restraintmask=':1-216',
> nstlim = 12500, dt = 0.002,
> temp0 = 300.0, tempi = 100.0,
> ntt = 1, vlimit = 20.0,
> ntp = 1, npscal = 1,
> ntc = 2, tol = 0.00001, pres0=1, comp=44.6,
> taup=2, tautp=1, jfastw=0,
> /
> &ewald
> use_pme=0, vdwmeth=0, eedmeth=4,ischrgd=1,
> /
> &wt
> type='TEMP0', istep1=0, istep2=5000,
> value1=100.0, value2=300.0,
> /
> &wt
> type='TEMP0', istep1=5000, istep2=12500,
> value1=300.0, value2=300.0,
> /
> &wt
> type='END',
> /
> /
> &rst
> iat=0,
> /
> error in reading namelist cntrl
> Dr. Maciej Maslyk
> Universidad San Pablo CEU
> Urb. Montepríncipe, Ctra. Boadilla del Monte,
> Km. 5.300, 28668 Madrid, Espańa
> Tel.- 91.372.64.31 - FAX.- 91.351.04.75
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jan 20 2010 - 09:00:03 PST
