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<<
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php