AMBER Archive (2006)

Subject: AMBER: md error : sander

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Sun May 28 2006 - 13:11:45 CDT

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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