[gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now

[Alan]

Hi there, in special Berk.

So pdb2gmx may be working with HIS and variants for oplsaa but now,
something that was working before is failing:

wget -c "http://www.pdbe.org/download/1BNA" -O 1BNA.pdb
grep 'ATOM  ' 1BNA.pdb >| DNA.pdb

cat << EOF >| SPE.mdp
define = -DFLEXIBLE
integrator               = md
nsteps                   = 0
dt                       = 0.001
constraints              = none
emtol                    = 10.0
emstep                   = 0.01
nstcomm                  = 1
ns_type                  = simple
nstlist                  = 0
rlist                    = 0
rcoulomb                 = 0
rvdw                     = 0
Tcoupl                   = no
Pcoupl                   = no
gen_vel                  = no
nstxout                  = 1
pbc                      = no
nstlog = 1
nstenergy = 1
nstvout = 1
nstfout = 1
nstxtcout = 1
comm_mode = ANGULAR
continuation = yes
EOF

pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p
DnaAmberSBGMX45
[snip]
8 out of 8 lines of specbond.dat converted successfully
[1]    42209 segmentation fault  pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb
-ff amber99sb -water none -p

with 5e347 it worded fine, i.e, it opens files

Opening force field file
/Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/aminoacids.arn
Opening force field file
/Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/dna.arn
Opening force field file
/Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/rna.arn

and proceed.

Alan
-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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