Hi Jason,
I re-generated the system psf using charmm.
It still did not work, but now the problem is somewhat different.
My system has protein, cholesterol, POPC, water and ions.
For each component, conversion from psf to AMBER was successful.
Two-components-system that has non-water component and water also worked.
But any other combination (protein+cholesterol, etc. ) failed due to either
segmentation fault or "topology file ends without finding all atom types",
which does not make sense.
I was wondering if chamber is indeed capable of converting a system
containing more than one non-water components.
Thanks!
On Fri, Feb 14, 2014 at 11:24 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Fri, 2014-02-14 at 11:15 -0500, Yi Shang wrote:
> > Hi there,
> > I was trying to prepare AMBER simulation with charmm ff.
> > I built the system .psf file using VMD, but then I am stuck trying to
> > convert .psf to AMBER topology using chamber.
>
> This is a known limitation of chamber (at least known to my experience).
> As a general rule, I think it's safe to assume that only CHARMM PSFs
> will work with chamber (i.e., not XPLOR or VMD-generated PSFs).
>
> >
> > To narrow down the problem, I did the following testing:
> >
> > A. I built a toy system containing only several ions. I got the following
> > error:
> >
> > $ chamber -top top_all36_combine.rtf -param par_all36_combine.prm -psf
> > ion.psf -crd ion.pdb -nocmap
> >
> > | *****************************************************
> > | * CHAMBER: Charmm psf to AMBER prmtop convertor *
> > | * *
> > | * v1.0 *
> > | * *
> > | * Written by: *
> > | * Mark J. Williamson *
> > | * Michael F. Crowley *
> > | * Ross C. Walker *
> > | * *
> > | *****************************************************
> >
> > forrtl: severe (64): input conversion error, unit 20, file XXXX/ion.psf
> > Image PC Routine Line
> Source
> >
> > libintlc.so.5 00007F1D7D5BBA7A Unknown Unknown
> Unknown
> > libintlc.so.5 00007F1D7D5BA576 Unknown Unknown
> Unknown
> > libifcore.so.5 00007F1D7E59680C Unknown Unknown
> Unknown
> > libifcore.so.5 00007F1D7E508DB2 Unknown Unknown
> Unknown
> > libifcore.so.5 00007F1D7E508256 Unknown Unknown
> Unknown
> > libifcore.so.5 00007F1D7E544400 Unknown Unknown
> Unknown
> > chamber 000000000042EA6A Unknown Unknown
> Unknown
> > chamber 0000000000401A6C Unknown Unknown
> Unknown
> > chamber 000000000040134C Unknown Unknown
> Unknown
> > libc.so.6 00007F1D7D01ECDD Unknown Unknown
> Unknown
> > chamber 0000000000401249 Unknown Unknown
> Unknown
> >
> >
> > B. I used .psf and .pdb from VMD online tutorial (psf generated using
> VMD).
> > I got exactly the same error message as test A.
> > $ chamber -top top_all36_combine.rtf -param par_all36_combine.prm -psf
> > kcsav.psf -crd kcsav.pdb -nocmap
> >
> > C. I used .psf and .pdb downloaded from charmm-gui website. These files
> > worked fine and I get prmtop and inpcrd generated.
> > $ chamber -top top_all36_combine.rtf -param par_all36_combine.prm -psf
> > step4_lipid.psf -crd step4_lipid.pdb -nocmap
> >
> > It seems to be the problem of reading VMD outputs, but the error message
> > from chamber is not enough for me to locate the problem. I was wondering
> if
> > anyone had the same issue before.
> >
> > Please find the inputs I used here (2MB in size, not allowed to be
> attached
> > here):
> > https://dl.dropboxusercontent.com/u/76890735/chamber.tar.gz
> >
> > Thank you in advance!
> >
> >
> > On Fri, Feb 14, 2014 at 12:02 AM, Yi Shang <mirandaisbest.gmail.com>
> wrote:
> >
> > > Hi there,
> > > I was trying to prepare AMBER simulation with charmm ff.
> > > I built the system .psf file using VMD, but then I am stuck trying to
> > > convert .psf to AMBER topology using chamber.
> > >
> > > To narrow down the problem, I did the following testing:
> > >
> > > A. I built a toy system containing only several ions. I got the
> following
> > > error:
> > >
> > > $ chamber -top top_all36_combine.rtf -param par_all36_combine.prm -psf
> > > ion.psf -crd ion.pdb -nocmap
> > >
> > > | *****************************************************
> > > | * CHAMBER: Charmm psf to AMBER prmtop convertor *
> > > | * *
> > > | * v1.0 *
> > > | * *
> > > | * Written by: *
> > > | * Mark J. Williamson *
> > > | * Michael F. Crowley *
> > > | * Ross C. Walker *
> > > | * *
> > > | *****************************************************
> > >
> > > forrtl: severe (64): input conversion error, unit 20, file XXXX/ion.psf
> > > Image PC Routine Line
> Source
> > >
> > > libintlc.so.5 00007F1D7D5BBA7A Unknown Unknown
> Unknown
> > > libintlc.so.5 00007F1D7D5BA576 Unknown Unknown
> Unknown
> > > libifcore.so.5 00007F1D7E59680C Unknown Unknown
> Unknown
> > > libifcore.so.5 00007F1D7E508DB2 Unknown Unknown
> Unknown
> > > libifcore.so.5 00007F1D7E508256 Unknown Unknown
> Unknown
> > > libifcore.so.5 00007F1D7E544400 Unknown Unknown
> Unknown
> > > chamber 000000000042EA6A Unknown Unknown
> Unknown
> > > chamber 0000000000401A6C Unknown Unknown
> Unknown
> > > chamber 000000000040134C Unknown Unknown
> Unknown
> > > libc.so.6 00007F1D7D01ECDD Unknown Unknown
> Unknown
> > > chamber 0000000000401249 Unknown Unknown
> Unknown
> > >
>
> This is a result of trying to read a string into an integer variable, or
> something of that nature. Since none of the read() statements are
> error-protected, hunting down which read caused the error might be
> laborious. One thing you can try is to build without optimization and
> with debug symbols and hope it gives a more reasonable traceback.
>
> If you do get VMD PSFs to work, we would greatly appreciate a patch or
> some type of recipe to get it working.
>
> Good luck!
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Yi Shang, Ph.D.
postdoctoral research associate
Icahn School of Medicine at Mount Sinai
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Feb 23 2014 - 22:00:02 PST
