Thanks for the files. Turns out the Amber restart file plugin for VMD
is broken. It chokes if time/temperature are specified after the
number of atoms (at least in version 1.9.2). You can still use cpptraj
to generate the restart file but you need to do it with 'trajout' and
the keywords 'notime' and 'notemperature'. The following will generate
a restart that VMD will read:
parm state00.parm7
trajin frame.nc
trajout test.rst7 notemperature notime
Hope this helps,
-Dan
On Fri, Feb 24, 2017 at 9:42 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> CPPTRAJ writes correctly formatted Amber restart files, and I have never had
> a problem getting VMD to read them. What versions of CPPTRAJ and VMD are you
> using? Those numbers aren't extra - they are number of atoms and time and
> are specified in the format: http://ambermd.org/formats.html#restart. (Note
> that there is actually a third element, temperature, that is used for REMD
> restarts). Can you send me off list the topology and restart in question so
> I can test? Thanks,
>
> -Dan
>
> On Thu, Feb 23, 2017 at 10:43 AM Elisa Pieri <elisa.pieri90.gmail.com>
> wrote:
>>
>> Uh, thanks! Easier than expected! I took the main structure from the
>> manual
>> examples, I don't know if the same correction should be applied to the
>> manual..
>> BTW, I discovered that the RST7 was unreadable for VMD just because on
>> line
>> 2 cpptraj adds two numbers (energy and force?) after the number of atoms;
>> another possible bug to be fixed?
>>
>> Thank you!
>> Elisa
>>
>> On Thu, Feb 23, 2017 at 4:36 PM, Nhai <nhai.qn.gmail.com> wrote:
>>
>> > Hi
>> >
>> > Change coords to coordinates.
>> >
>> > Hai Nguyen
>> >
>> > > On Feb 23, 2017, at 10:05 AM, Elisa Pieri <elisa.pieri90.gmail.com>
>> > wrote:
>> > >
>> > > coords
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Feb 24 2017 - 11:30:03 PST
