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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Received on Mon Feb 23 2015 - 05:30:03 PST
