AMBER Archive (2007)

Subject: Re: AMBER: SMD simulation

From: Qiang Zhong (zqiang320_at_webmail.hzau.edu.cn)
Date: Sat Aug 25 2007 - 04:49:09 CDT

>From: Adrian Roitberg <roitberg_at_qtp.ufl.edu>
>Reply-To: amber_at_scripps.edu
>To: amber_at_scripps.edu
>Subject: Re: AMBER: SMD simulation
>Date:Fri, 24 Aug 2007 08:43:35 -0400
>
>Qiang and all,
>
> When the amber errors say:
> "Cannot match namelist object name ¡¯dumpfreq¡¯,"
> you should find out if YOUR input has anything like that.
>
> In Qiang's case, it does.
>
> &wt type=¡¯DUMPFREQ¡¯, istep1=1, /
>
>
> I do not know where the extra symbols come from, but they should not be
> there.
>
> It should just be:
>
> &wt type=DUMPFREQ, istep1=1, /
>
> Same with the other errors.
> a.
>
Yes, I do as you say,I change smd.in just like 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=CaMKIIADP.RST
DUMPAVE=dist_vs_t
LISTIN=POUT
LISTOUT=POUT

But error change to:

Cannot match namelist object name dumpfreq,
Cannot match namelist object name end,
Cannot match namelist object name dumpfreq,

>
>
>
>
>
> Qiang Zhong wrote:
> > 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¡¯
> >
> >
> >
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project and Department of Chemistry
>
> University of Florida PHONE 352 392-6972
> P.O. Box 118435 FAX 352 392-8722
> Gainesville, FL 32611-8435 Email adrian_at_qtp.ufl.edu
> ============================================================================
>
> To announce that there must be no criticism of the president,
> or that we are to stand by the president right or wrong,
> is not only unpatriotic and servile, but is morally treasonable
> to the American public."
> -- Theodore Roosevelt
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu