AMBER Archive (2004)

Subject: Re: AMBER: Namelist problem

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Mon Jul 05 2004 - 08:10:51 CDT

Hi,
 no its not because there is a space before each of these.
thanks anyway for looking at it
Vlad

Guanglei Cui wrote:

> Hi,
>
> It's just a guess. Is it because of the missing space before &cntrl,
> &end, &wt, &rst?
>
> Guanglei
>
> 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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-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
home tel: ++49-551-9963204  

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