Thanks there Dan,
The netCDF (.ncrst) method worked well as I just tried.
Sent from my iPhone
> On Aug 12, 2020, at 11:05 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Glad you figured it out. One other option (if you're not on windows)
> is to convert to a NetCDF restart format (extension .ncrst) and use
> that instead.
>
> -Dan
>
>> On Wed, Aug 12, 2020 at 12:00 PM Liao <liaojunzhuo.aliyun.com> wrote:
>>
>> Hi there, thanks for response, comparing tleap rst7 and cpptraj rst7 is certainly a useful idea.
>>
>> I found from the VMD forum an answer to this problem of mine, that it involves a single number in the cpptraj rst7 file that needs to be deleted. It seems to be a known bug for VMD 1.9.3. The second number (number of picoseconds) on the second line of the file needs to be deleted by a text editor, and then VMD can load it properly. Probably people compared different versions of rst7 files and found out this reason.
>>
>> https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/29804.html
>>
>> And it worked in my case.
>>
>> Sent from my iPhone
>>
>>>> On Aug 12, 2020, at 1:06 AM, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>>>
>>> I have not dumped a full trajectory as rst7 files though I have used cpptraj to convert between netcdf and rst7.
>>>
>>>> But when I use VMD to try to open each rst7 and view them, nothing loads. VMD doesn’t give an error message either.
>>>
>>> When you are loading the files with VMD, are you loading them into the correct topology (prmtop) file? (vmd -f filename.prmtop -rst7 filename.rst). The restart files themselves contain coordinates, without anything to apply those coordinates to, VMD would probably not visualise anything useful.
>>>
>>>> I also realize that the rst7 file (1.2MB) size is different from the one generated by tleap (1.5MB).
>>>
>>> I have not used tleap to generate restart files before either so I don’t know the format.
>>>
>>> If you try to do
>>>
>>> file filename.rst7
>>>
>>> on the files you created, are they presented as ASCII text files? Alternatively, if you open them, can you read the content or is it just a bunch of gibberish? It is possible that you have not created ASCII RST7 text-files but most likely some of the newer binary formats, which could explain why they are smaller. In that case you may ned to specify the format of output directly instead of being interpreted from filename. Another simple check would be to do a diff:
>>>
>>> diff -y —supress-common tleapfile.rst7 cpptrajfile.rst7
>>>
>>> and check the differences. Or just open both the files and see if there is any obvious difference.
>>>
>>> Best regards
>>> // Gustaf
>>>
>>>> On 11 Aug 2020, at 23:47, Liao <liaojunzhuo.aliyun.com> wrote:
>>>>
>>>> Hi Amber users,
>>>>
>>>> Just discovered that cpptraj can write out Amber restart files (.rst7), something extremely useful.
>>>>
>>>> So I try to do it, trajin 16 frames from a trajectory, and use “trajout output.rst7 nobox” as the final command to get my rst7 files, it successfully generates 16 files.
>>>>
>>>> But when I use VMD to try to open each rst7 and view them, nothing loads. VMD doesn’t give an error message either.
>>>>
>>>> I also realize that the rst7 file (1.2MB) size is different from the one generated by tleap (1.5MB).
>>>>
>>>> Am I doing something wrong, is cpptraj capable of generating rst7 files from an Amber trajectory?
>>>>
>>>> Please help,
>>>> Thanks very much.
>>>>
>>>>
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Received on Wed Aug 12 2020 - 11:30:02 PDT
