FYI: buildprotein.F: got logical instead of integer
Patrick Schopf
I checked out the latest version of PMS via subversion from googlecode
and compiled the code with
fflags = -m64 -O3 -msse2 -mfpmath=sse -I. -fomit-frame-pointer -ffixed-
line-length-none -Wall -Werror
using gfortran on the new iridis3 cluster.
When I did a fakesim ProtoMS came up with the following error:
"At line 121 of file buildprotein.F
Fortran runtime error: Expected INTEGER for item 6 in formatted
transfer, got LOGICAL
("Bond ",i3,1x,2(a,1x),i5,1x,i1)"
I was firstly surprised not to find this warning in the warnings file
created by PMS, nor does the simulation break. In fact it terminates
without any further notice. So I thought this might be a read-in error
of my particular protein setup, so I started using different proteins
from the
ProtoMS tutorials section. I found that any protein I load up will
give this same error message. As an example
I have used the following input.cmd and files from tutorials/protoms-
cox2/single-prot:
# Parameter files
parfile1 parameter/amber99.ff
parfile2 parameter/solvents.ff
parfile3 parameter/amber99-residues.ff
parfile4 parameter/gaff.ff
parfile5 in/lig8t1bound.template
# PDB Files
solute1 in/lig8t1.pdb
solvent1 in/COX2-watercapbound.pdb
protein1 in/COX2-scoop1510-neutral.pdb
#set the output files
streamwarning warning
streamfatal fatal
streamheader off
streaminfo on
streamdetail on
streamaccept on
streamresults on
cutoff 10.00
feather 0.5
prefsampling 1 200.0
chunk1 fakesim
chunk2 results write
As the subject says this is FYI; I will follow this issue and send an
update if I find what exactly causes this message, but if anyone has
already experienced and solved this I would be grateful for any
pointers into the right direction.
Patrick
Christopher Woods
The problem is seen on some fortran compilers - they seem unable to
automatically convert a logical to an integer for printing, so just
crash the program (hence the error is written by the fortran support
library, not by protoms). I've fixed the bug and have updated the
repository. Do "svn update" and then recompile and the problem should
be fixed.
Christopher