Hi
try like this to combine MDCRD files in to one mdcrd file
create a input file name --> combine_mdcrds&strip.ptraj
=============================
trajin production_md1.mdcrd.gz
trajin production_md2.mdcrd.gz
trajin production_md3.mdcrd.gz
trajin production_md4.mdcrd.gz
trajin production_md5.mdcrd.gz
trajin production_md6.mdcrd.gz
trajin production_md7.mdcrd.gz
trajin production_md8.mdcrd.gz
trajin production_md9.mdcrd.gz
trajin production_md10.mdcrd.gz
trajout production_all_no_wat.mdcrd
rms first out production_all.rmsfit @N,CA,C time 1
center :1-20
image familiar
strip :WAT
command
=============================
cpptraj -p production_wat.prmtop -i combine_mdcrds&strip.ptraj
also you can have a look in to this link
http://structbio.vanderbilt.edu/archives/amber-archive/2008/0019.php
Yes VMD can view the netCDF file but you need to install netCDF plugin in
to VMD.(some where I read in the forum, i guess some one already answered
this question)
Cheers
Vince
On 25 October 2015 at 21:47, Soumendranath Bhakat <
bhakatsoumendranath.gmail.com> wrote:
> 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.
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> 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/
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 26 2015 - 02:30:03 PDT
