[gmx-users] gmx 4.5 issue with grompp

[Alan]

I am trying this test of mine:


wget -c "
http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1BVG"
-O 1BVG.pdb
grep 'ATOM  ' 1BVG.pdb>| Protein.pdb

pdb2gmx -ff amber99sb -f Protein.pdb -o Protein2.pdb -p Protein.top -water
spce -ignh

editconf -bt triclinic -f Protein2.pdb -o Protein3.pdb -d 1.0

genbox -cp Protein3.pdb -o Protein_b4ion.pdb -p Protein.top -cs

cat << EOF >| em.mdp
define                   = -DFLEXIBLE
integrator               = cg ; steep
nsteps                   = 200
constraints              = none
emtol                    = 1000.0
nstcgsteep               = 10 ; do a steep every 10 steps of cg
emstep                   = 0.01 ; used with steep
nstcomm                  = 1
coulombtype              = PME
ns_type                  = grid
rlist                    = 1.0
rcoulomb                 = 1.0
rvdw                     = 1.4
Tcoupl                   = no
Pcoupl                   = no
gen_vel                  = no
nstxout                  = 0 ; write coords every # step
optimize_fft             = yes
EOF

cat << EOF >| md.mdp
integrator               = md
nsteps                   = 1000
dt                       = 0.002
constraints              = all-bonds
nstcomm                  = 1
ns_type                  = grid
rlist                    = 1.2
rcoulomb                 = 1.1
rvdw                     = 1.0
vdwtype                  = shift
rvdw-switch              = 0.9
coulombtype              = PME-Switch
Tcoupl                   = v-rescale
tau_t                    = 0.1 0.1
tc-grps                  = protein non-protein
ref_t                    = 300 300
Pcoupl                   = parrinello-rahman
Pcoupltype               = isotropic
tau_p                    = 0.5
compressibility          = 4.5e-5
ref_p                    = 1.0
gen_vel                  = yes
nstxout                  = 2 ; write coords every # step
lincs-iter               = 2
DispCorr                 = EnerPres
optimize_fft             = yes
EOF

grompp -f em.mdp -c Protein_b4ion.pdb -p Protein.top -o Protein_b4ion.tpr
\cp Protein.top Protein_ion.top

echo 13 | genion -s Protein_b4ion.tpr -o Protein_b4em.pdb -neutral -conc
0.15 -p Protein_ion.top -norandom

\mv Protein_ion.top Protein.top

grompp -f em.mdp -c Protein_b4em.pdb -p Protein.top -o em.tpr

mdrun -v -deffnm em

grompp -f md.mdp -c em.gro -p Protein.top -o md.tpr

And it fails for the command above with:

-------------------------------------------------------
Program grompp, VERSION 4.5-beta1
Source code file: inputrec.c, line: 161

Software inconsistency error:
Unknown epc value


Any ideas? Thanks,

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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