May be like this
file name conversion.ptrj
trajin md_dry.mdcrd
trajout md_dry.nc
use command cpptraj stripped.com_solvated.top conversion.ptrj
On Sun, Oct 25, 2015 at 8:51 PM, Nhai <nhai.qn.gmail.com> wrote:
>
> > 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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>
--
Thanks & Regards;
Soumendranath Bhakat
Doctoral Student, Division of Biophysical Chemistry, CMPS, Lund University,
Sweden
Homepage: https://cbiores.wordpress.com/
ResearchGate: https://www.researchgate.net/profile/Soumendranath_Bhakat2
Google Scholar: http://scholar.google.com/citations?user=Q1_nDMcAAAAJ&hl=en
Past: Molecular Modelling and Drug Design Research Group
Discipline of Pharmaceutical Sciences
UKZN, Westville
Weblink: http://soliman.ukzn.ac.za/Home.aspx
and Department of Pharmaceutical Sciences
Birla Institute of Technology, Mesra, India
in.linkedin.com/pub/soumendranath-bhakat/15/79b/b9/
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Received on Sun Oct 25 2015 - 14:00:04 PDT
