Re: [AMBER] CHAMBER with RNA

From: BERGY <nucleic81.gmail.com>
Date: Fri, 29 Jun 2012 12:58:15 +0530

HI All,

I tried to run chamber for RNA duplex. i could not make it run, got the
same error as stated above. attaching the error and files,script used .

bergy.new:~/chamber$ chamber -top top_all27_na.rtf -param
par_all27_na.prm -psf out.psf -crd out.pdb -p out.prmtop -inpcrd
out.inpcrd -nocmap

| *****************************************************
| * CHAMBER: Charmm psf to AMBER prmtop convertor *
| * *
| * v1.0 *
| * *
| * Written by: *
| * Mark J. Williamson *
| * Michael F. Crowley *
| * Ross C. Walker *
| * *
| *****************************************************


===========================================================
          PSF input parsing summary
===========================================================

                        Number of PSF flags found: 1

                            Number of atoms found: 2113
                         Number of residues found: 66

                            Number of bonds found: 2277
                           Number of angles found: 4073
                        Number of dihedrals found: 6067
                        Number of impropers found: 166

                           Number of donors found: 199
                        Number of acceptors found: 561
    Number of explicit nonbonded exclusions found: 0

                           Number of groups found: 265
                       Number of ST2 waters found: 0

===========================================================

   --- Found all ATOM TYPES in topology file

   --- Found all nonbond parameters
At line 893 of file psfprm.F90
Fortran runtime error: Bad value during floating point read




On Tue, May 8, 2012 at 4:41 PM, Mark Williamson <mjw.mjw.name> wrote:

> On 03/05/12 16:16, Sean Law wrote:
> >
> > This is as far as I have reached without digging into the CHAMBER source
> code so any suggestions, comments, or hints would be greatly appreciated.
> > Thank you for your time.
> > Sean
>
> Dear Sean,
>
> Please can you prepare a test case containing all the input files, a
> script executing the relevant commands to reproduce what you see and
> then tar+bzip2 all this up into a .tar.bz2 file. Finally, can you email
> it to me offlist so that I can reproduce the problem and then attempt to
> debug it.
>
> Thanks,
>
> Mark
>
>
>
> _______________________________________________
> 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 Fri Jun 29 2012 - 00:30:02 PDT
Custom Search