AMBER Archive (2006)

Subject: Re: AMBER: md error : sander

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Sun May 28 2006 - 15:06:21 CDT

I don't think npscal exists in amber9, do you find it in
the manual?

Did you try running without this? (since the error message is pretty
clear)

jitrayut jitonnom wrote:

> Dear amber members
> I have a problem when I tried to run md simulation of protein-protein
> complex. I don't know this is the error about my input file or amber9
> installation. So, I will appreciate if anyone can answer me.
>
> This is the result :-
>
> [jitrayut_at_localhost enz_complex_ph7_1n]$ sander -O -i md_500ps.in -o
> dock71_md500ps.out -p dock71.top -c dock71.rst -r dock71_md500ps.rst
> -x dock71_md500ps.mdcrd &
> [1] 5097
> [jitrayut_at_localhost enz_complex_ph7_1n]$ At line 896 of file _mdread.f
> (Unit 5 "md_500ps.in")
> Traceback: not available, compile with -ftrace=frame or -ftrace=full
> Fortran runtime error: In line 1 of namelist cntrl:
> Namelist variable 'npscal' not found
> taup = 0.2, npscal
>
> and the input file is here :
>
> #Heating the system 0-300K in 60 ps, 300-300K from 61-20000 ps#
>
> &cntrl
>
> nmropt = 1,
>
> ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
>
> ntpr = 50, ntwx = 50, ntwv = 0, ntwe = 0,
>
> ntf = 2,
>
> cut = 8.0, nsnb = 10,
>
> nstlim = 250000,
>
> t = 0.0, dt = 0.002,
>
> temp0 = 300.0, tempi = 0.0,
>
> ig = 71784, heat = 0.0,
>
> ntt = 1,
>
> tautp = 0.2,
>
> vlimit = 20.0,
>
> ntb = 1, ntp = 0, pres0 = 1.0, comp = 44.6,
>
> taup = 0.2, npscal = 1,
>
> ntc = 2, tol = 0.0005,
>
> &end
>
> &wt
>
> type='TEMP0', istep1=0, istep2=30000,
>
> value1=0.0, value2=300.0,
>
> &end
>
> &wt
>
> type='TEMP0', istep1=30000, istep2=250000,
>
> value1=300.0, value2=300.0,
>
> &end
>
> &wt
>
> type='END',
>
> &end
>
> &rst
>
> iat=0,
>
> &end
>
>
> ,Thanks
>
> Jitrayut Jitonnom
> Chiang Mai University
> Thailand
> 50200
>
> Tel : (+66) 6 613-4218

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