Can I use netcdf trajectory file for mmpbsa/mmgbsa calculation?
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 - 11:00:04 PDT
