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
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Received on Fri Feb 14 2014 - 08:30:03 PST
