AMBER Archive (2007)

Subject: AMBER: SMD simulation

From: Qiang Zhong (zqiang320_at_webmail.hzau.edu.cn)
Date: Fri Aug 24 2007 - 05:33:41 CDT

Dear Amber Users:
           I am doing SMD simulation, I got some error message,
Could somebody tell me what wrong with it.Thank you very much!

[internet_at_localhost sample_0]$ sander -O -i ../../prm/smd.in -p ../xxx.parm7 -c
../xxx_eq_v.rst -r xxx_push.rst -x xxx_push.crd -o xxx_push.out
Cannot match namelist object name ¡¯dumpfreq¡¯,
Cannot match namelist object name ¡¯end¡¯,
Cannot match namelist object name ¡¯dumpfreq¡¯,

my parameter file is below:

<smd.in>
 Sample pulling input
&cntrl
  nstlim=1000, cut=99.0, igb=1, saltcon=0.1,
  ntpr=100, ntwr=100000, ntt=3, gamma_ln=5.0,
  ntx=5, irest=1, ntwx=100000000, ig = 256251,
  ntc=2, ntf=2, tol=0.000001,
   dt=0.002, ntb=0, tempi=300., temp0=300.,
   jar=1,
 /
 &wt type=¡¯DUMPFREQ¡¯, istep1=1, /
 &wt type=¡¯END¡¯, /
DISANG=dist.RST
DUMPAVE=dist_vs_t
LISTIN=POUT
LISTOUT=POUT

<dist.RST>
# Change distance between group2 and atom CA from 18 A to 8 A
&rst iat=4269,-1, r2=18., rk2 = 5000., r2a=8. /
igr1 = 0,igr2 = 4750,4751,0,
grnam2(1)=¡¯PB¡¯,grnam2(2)=¡¯O2B¡¯

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