Re: [AMBER] strange format of .rst file

From: Thakur, Abhishek <axt651.miami.edu>
Date: Fri, 18 Nov 2016 17:04:15 +0000

Thank you

But after converting it to ascii format I am trying to make pdb file from the .rst file I am getting an error

Error: '*' encountered (atom 10706 Y). This indicates coordinate overflow.



________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Friday, November 18, 2016 5:20:42 AM
To: AMBER Mailing List
Subject: Re: [AMBER] strange format of .rst file

ntxo=2 is the amber netcdf restart format. This is a binary format, i.e. it
is not human-readable. If for some reason you want it converted back to
ascii, you can use something like:

cpptraj -p topology.parm7 -y netcdf.restart -x ascii.rst7

However, in most cases this is unnecessary.

-Dan

On Fri, Nov 18, 2016 at 8:54 AM Thakur, Abhishek <axt651.miami.edu> wrote:

> Hi everyone,
>
> Earlier while working of GB/SA calculation I had a problem in which my
> simulation stopped as it was unable to read some line in my .rst file.
>
> So as per earlier comment from Dr.Daniel Roe
> https://urldefense.proofpoint.com/v2/url?u=http-3A__archive.ambermd.org_201310_0426.html&d=DgIGaQ&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=G2ulLEHCJO2YKq6do6rSJxdGu6d3NAouMLUwG-Ps7Rk&s=Rms6TP9iS4gHh2CLRCpJg2ubLO91nqvjQx6zELRe-TI&e=
>
> I have made ntxo=2, But after that I can find that my .rst file has given
> me output something like this
>
> CDF^B^.^.^.^.^.^.^.
>
> ^.^.^.^B^.^.^.^Gspatial^.^.^.^.^C^.^.^.^Datom^.^.)^.^.^.^L^.^.^.^F^.^.^.^Etitle^.^.^.^.^.^.^B^.^.^.^Ldefault_name^.^.^.^Kapplication^.^.^.^.^B^.^.^.^EAMBER^.^.^.^.^.^.^Gprogram^.^.^.^.^B^.^.^.^Epmemd^.^.^.^.^.^.^NprogramVersion^.^.^.^.^.^B^.^.^.^D14.0^.^.^.^KConventions^.^.^.^.^B^.^.^.^LAMBERRESTART^.^.^.^QConventionVersion^.^.^.^.^.^.^B^.^.^.^C1.0^.^.^.^.^K^.^.^.^D^.^.^.^Dtime^.^.^.^.^.^.^.^L^.^.^.^A^.^.^.^Eunits^.^.^.^.^.^.^B^.^.^.
>
>
> I am unable to get what is this and how to convert it back
>
>
>
> with regards,
>
> Abhishek
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DgIGaQ&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=G2ulLEHCJO2YKq6do6rSJxdGu6d3NAouMLUwG-Ps7Rk&s=fZWteE0RSjrqLT6P1EXS_UeJ8xcScycO0_eN_1dY0C0&e=
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DgIGaQ&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=G2ulLEHCJO2YKq6do6rSJxdGu6d3NAouMLUwG-Ps7Rk&s=fZWteE0RSjrqLT6P1EXS_UeJ8xcScycO0_eN_1dY0C0&e=
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 18 2016 - 09:30:03 PST
Custom Search