After installing the setup.py I tried with following command
COMMAND:
$AMBERHOME/ParmEd-master/parmed.py -top top_all36_cgenff.rtf -param
par_all36_prot.prm -psf 2rf9_noh_autopsf.psf -crd 2rf9_noh_autopsf.pdb -p
prot.prmtop -inpcrd prot.inpcr
ERROR:
parmed.py: error: unrecognized arguments: -top par_all36_prot.prm
2rf9_noh_autopsf.psf 2rf9_noh_autopsf.pdb prot.inpcr
On Mon, Feb 23, 2015 at 6:56 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Mon, 2015-02-23 at 18:19 +0530, vijay kumar narsapuram wrote:
> > Hello sir,
> >
> > I have successfully installed ambertools in my system.
> >
> > Actually I need to calculate free energy using mm-pbsa in ambertools,
> but i
> > have trajectories which are simulated using amber CHARMM force field.
> So, i
> > thought i would follow below steps.
> >
> > 1) Generate your PSF file using whatever tool necessary
> > 2) Run a simulation in NAMD with this PSF file.
> > 3) Use chamber to generate a topology file compatible with cpptraj,
> sander,
> > and pmemd from the PSF file you generated in step 1. (You also need to
> > create the complex, receptor, and ligand topology files)
> > 4) Run MMPBSA.py using the chamber-generated topology files you created
> in
> > step 3 with the DCD file you created in step 2.
> >
> > when I ran chamber command mentioned below:
> >
> > $AMBERHOME/bin/chamber -cmap -top top_all27_prot_na.rtf -param
> > par_all36_prot.prm
>
> Don't do this! You are mixing the RTF file from CHARMM 27 with the
> parameter file from CHARMM 36. This is a *bad* idea.
>
> > -str par_all27_prot_na.prm -str top_all36_cgenff.rtf
> > -psf 2rf9_noh_autopsf.psf -crd 2rf9_noh_autopsf.pdb -p prot.prmtop
> -inpcrd
> > prot.inpcrd
> >
> > ERROR:
> > At line 2349 of file psfprm.F90 (unit = 20, file =
> '2rf9_noh_autopsf.psf')
> > Fortran runtime error: Bad value during integer read
> >
> >
> > Then after watching for suggestions regarding this error. I found that,
> we
> > can even use PRAMED for generating amber compatable toplogy files.but
> when
> > I saw amber doc file for details it was mentioned that some parmed script
> > needed to run the command which i could not found..
> >
> > can please help me in this regard finding script and proper command which
> > would provide me .prmtop and .inpcrd.
>
> The version of ParmEd that can generate chamber topology files is coming
> out in April with the next release of AmberTools. You can download a
> version that *does* have this capability from Github:
> https://github.com/ParmEd/ParmEd. I suggest downloading the ZIP file.
> Unzip it, change to that directory, and type:
>
> python setup.py install --prefix=$AMBERHOME/
>
> This will install it to $AMBERHOME. Then you can use a very similar
> command in ParmEd as you did to run chamber in the shell. First thing
> you need to do, though, is make sure you're using the CHARMM force field
> correctly (i.e., do NOT mix-and-match different versions of the RTF and
> PAR files).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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>
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Received on Mon Feb 23 2015 - 07:00:02 PST
