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
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
>
>
> 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.
>
> Attached please find all the input files I used.
> Thank you in advance!
>
> --
> Yi Shang, Ph.D.
> postdoctoral research associate
> Icahn School of Medicine at Mount Sinai
>
>
>
--
Yi Shang, Ph.D.
postdoctoral research associate
Icahn School of Medicine at Mount Sinai
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Received on Fri Feb 14 2014 - 08:30:02 PST
