Dear Bill,
Thank you. I manually amended the NATOM in the 2nd line, and the script
works now.
Yes, indeed, the files has a big number of NATOM (i.e. 1040945 atoms). I
set the output now to netcdf (ntxo=2).
Thank you very much.
CS
On Tue, Feb 21, 2017 at 2:28 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> How many atoms in your system? Note the I5 format on the 2nd line of
> coordinate/restart:
>
> http://ambermd.org/formats.html#restart
>
> FORMAT(I5,5E15.7) NATOM,TIME
>
> If you have > 99999 atoms (5x'9'), netcdf format is your only hope.
>
> Bill
>
>
> On 2/20/17 10:19 PM, Bill Ross wrote:
> > How many fields have ****? If it's only on the 2nd line, it can probably
> > be fixed manually.
> >
> > Also you could try writing a netcdf rst.
> >
> > Bill
> >
> >
> > On 2/20/17 9:55 PM, Chinh Su Tran To wrote:
> >> Dear Bill,
> >>
> >> Thanks. Yes, it indeed is.
> >> I looked at the min1.rst in text editor, the 2nd line of the resulting
> >> min1.rst output contains ****, the rest looks normal. I couldn't view
> the
> >> structure as it couldn't be converted because some format errors
> occurred.
> >>
> >> I was searching for the cause behind since it is confusing to me that
> the
> >> bash script used for this run was applied previously and it worked.
> >>
> >> One note aside, in the beginning of the min1.out, there are some
> numerical
> >> errors (represented by **** in VDWAALS results, I guess that was caused
> by
> >> unreasonable distances in the initial structure, but it is resolved in
> the
> >> end of the first minimization min1). Hence, I think this is not the
> cause.
> >>
> >> Please help. Thanks.
> >>
> >> CS
> >>
> >>
> >>
> >> On Tue, Feb 21, 2017 at 11:50 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >>
> >>> It's the output of the run that created the .rst that needs looking at.
> >>>
> >>> Bill
> >>>
> >>>
> >>> On 2/20/17 7:33 PM, Hai Nguyen wrote:
> >>>> I didn't see any wrong in my input files.
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Received on Mon Feb 20 2017 - 23:30:02 PST
