AMBER Archive (2007)

Subject: Re: AMBER: invalid digit '*' in the input file

From: rebeca_at_mmb.pcb.ub.es
Date: Mon Nov 12 2007 - 08:56:26 CST

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_at_mmb.pcb.ub.es

Quoting Martin Klefas-Stennett <martin.stennett_at_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_at_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_at_mmb.pcb.ub.es
>>
>>
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