AMBER Archive (2004)

Subject: Re: AMBER: Namelist problem

From: Viktor Hornak (hornak_at_csb.sunysb.edu)
Date: Mon Jul 05 2004 - 09:07:36 CDT

Did you try '/' instead of '&end' ? Supposedly that's most complying to
the standard namelist conventions (see one of the appendices in amber8
manual). Also, restraintmask might need its argument to be enclosed in
quotes, such as restraintmask=":${RES1}-${RES2}" - but check your shell
expansion rules to make sure that it expands what you expect! (for
starter, I'd just replace that with specific numbers for the sake of
troubleshooting).

-Viktor

Vlad Cojocaru wrote:

> Dear Amber users,
> Could somebody give me a hint what's wrong with the input below.
> AMBER 8 on AIX exits with the error:
> 1525-049 The list-directed or NAMELIST READ statement cannot be
> completed because the input data did not specify a valid delimited
> character string. The program will recover by ignoring the item in
> the READ statement.
> ERROR: 0031-250 task 6: Terminated
> ERROR: 0031-250 task 2: Terminated
> ERROR: 0031-250 task 3: Terminated
> ERROR: 0031-250 task 7: Terminated
> ERROR: 0031-250 task 4: Terminated
> ERROR: 0031-250 task 0: Terminated
> ERROR: 0031-250 task 1: Terminated
> ERROR: 0031-250 task 5: Terminated
> I remember thatt for running Amber7 on AIX I had to add (export
> XLFRTEOPTS="namelist=old"). Is this change in Amber8???
> Thank you very much in advance
>
> cat << EOF > equil0${jequil1}.in
> ${fname}, equilibration GB run no. ${jequil1}, `date`
> &cntrl
> imin=0, nmropt=1, ntx=1, irest=0, ntxo=1, ntpr=50, ntwr=100,
> ntwx=100, ntwv=0, ntwe=0, ntf=1, ntb=0, cut=25.0,
> scnb=2.0, scee=1.2, igb=1, intdiel=1, extdiel=78.5, saltcon=0.0,
> rgbmax=25, rbornstat=0, offset=0.009, gbsa=0, surften=0.005,
> ntr=1, restraint_wt=500, restraintmask=:${RES1}-${RES2},
> nstlim=400000, t=0.0, dt=0.001,
> temp0=300.0, tempi=10.0, ntt=3, gamma_ln=5, vlimit=20.0, ntc=1,
> &end
> &wt type='TEMP0', istep1=0, istep2=20000, value1=10.0, value2=300.0, &end
> &wt type='TEMP0', istep1=20001, istep2=40000, value1=300.0,
> value2=300.0, &end
> &wt type='END', &end
> &rst iat=0, &end
> EOF
>

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