I found that this was caused when some of the atom positions became too
large to fit into the width of the output field assigned to them. When
writing the restart file sander had written ***** instead of a number
and when it re-imported the data I got the same messages as you.
My problem was cured by using iwrap=1 in all of my runs.
Martin
rebeca.mmb.pcb.ub.es wrote:
> Dear Amber users,
>
> I am having troubles with several AMBER calculations. Some of them finish with
> an error (in the error file) of the type of:
>
> 1525-097 A READ statement using decimal base input found the invalid digit '*'
> in the input file. The program will recover by assuming a zero in its place.
> 1525-097 A READ statement using decimal base input found the invalid digit '*'
> in the input file. The program will recover by assuming a zero in its place.
> 1525-097 A READ statement using decimal base input found the invalid digit '*'
> in the input file. The program will recover by assuming a zero in its place.
> (...)
> srun: error: s05c5b05: task[8-11]: Segmentation fault
> srun: Job Failed
>
> The input file is OK, since I have used it for the previous simulations:
>
> &cntrl
> imin=0,
> irest=1,
> ntx=7,
> ntb=2,
> cut=10,
> pres0=1.0,
> ntp=1,
> taup=2.0
> ntr=0,
> ntc=2,
> ntf=2,
> tempi=300.0,
> temp0=300.0,
> ntt=3,
> gamma_ln=0.1,
> nstlim=700000,
> dt=0.002,
> ntpr=1000,
> ntwx=1000,
> ntwr=1000
> /
>
> I am using Amber 9.0 and this error has appeared in several simulations that do
> not have anything to do between them.
>
> Has any of you had this type of problem in your simulations?
>
> Thanks a lot for your help in advance,
>
>
> Rebeca García Fandiño
> Parc Cientific de Barcelona
> Barcelona
> rebeca.mmb.pcb.ub.es
>
>
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Received on Wed Nov 14 2007 - 06:07:28 PST
