Thanks a lot for your suggestion,
as you mention the restart file sander have several **** instead of a number,
so that must be the cause of the problem. I will try iwrap=1.
Only one more question, should I restart all the simulation, or could I
begin to
use iwrap=1 just from now on, from the simulation that has failed, and mantain
the older ones with iwrap=0? Will ptraj post-processing will correct this
mixture and change translating molecules back to the primary box?
Thanks again for you help,
Rebeca García Fandiño
Parc Cientific de Barcelona
Barcelona
rebeca.mmb.pcb.ub.es
Quoting Martin Klefas-Stennett <martin.stennett.postgrad.manchester.ac.uk>:
> 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
