Since your input file works fine with other runs, it is not likely the
culprit.
Is it possible that the previous simulation left over-flow digits in the
coordinate file? You might open it and look for **** patterns. This can
happen if you have a simulation that drifts far from the (0,0,0)
coordinates. I suppose it might happen in a very ill-behaved minimization
as well.
If this were the case, then when FORTRAN substitutes (0,0,0) for (****,
****, ****) you have many overlapping atoms, and a segmentation fault
would be expected.
Chris'
> 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
