AMBER Archive (2007)

Subject: Re: AMBER: SMD simulation

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Fri Aug 24 2007 - 07:43:35 CDT

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.

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¡¯
>
>
>
>
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-- 
                            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
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