[AMBER] Problem with CHAMBER (for RNA molecule)

From: Marc van der Kamp <marcvanderkamp.gmail.com>
Date: Fri, 26 Oct 2012 09:59:17 +0100


We've been trying to prepare a system consisting of RNA strands for
simulation with the CHARMM27 nucleic acid force field.
Creation of a CHARMM .psf is successful.

However, when we try to generate a prmtop and inpcrd with CHAMBER, we are
running into problems.

When CHAMBER is run with a simple test case (2 strands of RNA and nothing
else) and using the standard CHARMM27 parameter and topolgy files as

 chamber -top top_all27_na.rtf -param par_all27_na.prm -psf test.psf -crd
test.crd -p test.prmtop -inpcrd test.inpcrd -cmap

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

Line 893 is a line for parsing dihedral parameters, reading the fifth
'word' [read(words(5) ...] in this section:

if(dihe_match(words(1:4)(1:idLen),attype_name(itt), &
                      attype_name(jtt),attype_name(ktt), &
                      attype_name(ltt))) then
                    read(words(5),'(g20.12)')pk00 !barrier height
                    read(words(6),'(i20)')ipn00 !perodicity
                    read(words(7),'(g20.12)')phase00 !phase angle

We aren't sure what is going wrong here.
As the above test uses the standard .prm and .rtf files that ship with
CHARMM, I think it is something that needs to be fixed in CHAMBER.

Thanks in advance for any help!
AMBER mailing list
Received on Fri Oct 26 2012 - 02:00:02 PDT
Custom Search