> On Oct 25, 2015, at 1:39 PM, shahab shariati <shahab.shariati.gmail.com> wrote:
>
> Can I use netcdf trajectory file for mmpbsa/mmgbsa calculation?
>
You should try by yourself, it is just a matter of changing filename if you want to do mmpba anyway.
For other questions, please try to copy and paste your questions to google first. I believe the answers are in first 5 links.
Hai
> On Sun, Oct 25, 2015 at 8:49 PM, shahab shariati <shahab.shariati.gmail.com>
> wrote:
>
>> I have obtained my mdcrd files using amber 10 and ambertools14.
>>
>> On Sun, Oct 25, 2015 at 8:46 PM, shahab shariati <
>> shahab.shariati.gmail.com> wrote:
>>
>>> Dear amber users,
>>>
>>> I have done many md simulations (protein-ligand complex) to obtain binding
>>> free energy using mmpbsa/mmgbsa methods.
>>>
>>> I have 4 production steps and subsequently 4 mdcrd trajectory files.
>>>
>>> I have not yet started mmpbsa/mmgbsa calculations.
>>>
>>> Unfortunately, I forgot to use ioutfm=1 in &cntrl section of the sander
>>> input file.
>>>
>>> I know the advantage of the NetCDF trajectory format than mdcrd
>>> trajectory format.
>>>
>>> Now, I want to convert my 4 mdcrd trajectory files to 1 netcdf trajectory
>>> file.
>>> How to do that?
>>>
>>> Can I view a netcdf trajectory file using VMD?
>>>
>>> Any help will highly appreciated.
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Received on Sun Oct 25 2015 - 13:00:03 PDT
