Hi Ross,
I think we have AmberTools13 on our server:
$ ./update_amber --version
Version is reported as <version>.<patches applied>
AmberTools version 13.22
Amber version 12.21
On Fri, Feb 14, 2014 at 1:29 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Chamber was supposed to have been updated to support XPLOR psf's:
>
> commit 32ca3f6ccf3b7262916be3d8ff679879914a7f7d
> Author: Mark Williamson <mw529.cam.ac.uk>
> Date: Fri Jun 3 10:47:50 2011 +0100
>
> Add support for VMD compatible CHAMBER prmtops
>
>
>
>
> Check that you are using a fully up to date version of chamber - from
> AmberTools13.
>
> Although it's possible that only worked for all22 and the issue is an
> incompatibility between all36 and VMD in chamber. For now if you have
> Charmm the workaround would be to load it into charmm and then resave the
> psf as a charmm format psf.
>
> if it is indeed a problem with all36 and VMD psfs then we'll have to take
> a look at fixing it but it might take a while.
>
> If you can confirm you are using the latest chamber from AmberTools13
> fully patched then I'll put this into our bugzilla so it doesn't lost.
>
> All the best
> Ross
>
>
>
>
> On 2/14/14, 8:24 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
>
>
>
> _______________________________________________
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> AMBER.ambermd.org
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>
--
Yi Shang, Ph.D.
postdoctoral research associate
Icahn School of Medicine at Mount Sinai
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Received on Fri Feb 14 2014 - 11:00:02 PST
