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 -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.
Thanks in advance
Regards
Vijay
On Mon, Feb 2, 2015 at 7:37 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> > On Feb 2, 2015, at 8:47 AM, vijay kumar narsapuram <nvijay1991.gmail.com>
> wrote:
> >
> > I am using ubuntu 13.04.
> >
> > which flex gave:/usr/local/bin/flex
>
> This is a problem. Where did this flex come from? What seems to have
> happened is that you installed something to /usr/local that includes a
> program called “flex” that is conflicting with the system flex inside
> /usr/bin.
>
> You need to make sure that when the “flex” program is run, the one inside
> /usr/bin/flex is used instead of /usr/local/bin/flex. You can do this in a
> couple ways:
>
> 1. Rearrange your PATH environment variable so that /usr/bin comes
> *before* /usr/local/bin.
> 2. Delete the /usr/local/bin/flex program (if you don’t need that program,
> this might be the best route)
> 3. Change “flex” in the config.h file to “/usr/bin/flex” to make sure it
> uses the “correct” program. I’m not positive that this will work, but if
> it does it would probably be the easiest option.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
> _______________________________________________
> 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 Feb 23 2015 - 05:00:02 PST
