I am trying this test of mine:<div><br></div><div><br></div><div><div>wget -c "<a href="http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1BVG">http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1BVG</a>" -O 1BVG.pdb</div>
<div>grep 'ATOM ' 1BVG.pdb>| Protein.pdb</div><div><br></div><div>pdb2gmx -ff amber99sb -f Protein.pdb -o Protein2.pdb -p Protein.top -water spce -ignh</div><div><br></div><div>editconf -bt triclinic -f Protein2.pdb -o Protein3.pdb -d 1.0</div>
<div><br></div><div>genbox -cp Protein3.pdb -o Protein_b4ion.pdb -p Protein.top -cs</div><div><br></div><div>cat << EOF >| em.mdp</div><div>define = -DFLEXIBLE</div><div>integrator = cg ; steep</div>
<div>nsteps = 200</div><div>constraints = none</div><div>emtol = 1000.0</div><div>nstcgsteep = 10 ; do a steep every 10 steps of cg</div><div>emstep = 0.01 ; used with steep</div>
<div>nstcomm = 1</div><div>coulombtype = PME</div><div>ns_type = grid</div><div>rlist = 1.0</div><div>rcoulomb = 1.0</div><div>rvdw = 1.4</div>
<div>Tcoupl = no</div><div>Pcoupl = no</div><div>gen_vel = no</div><div>nstxout = 0 ; write coords every # step</div><div>optimize_fft = yes</div>
<div>EOF</div><div><br></div><div>cat << EOF >| md.mdp</div><div>integrator = md</div><div>nsteps = 1000</div><div>dt = 0.002</div><div>constraints = all-bonds</div>
<div>nstcomm = 1</div><div>ns_type = grid</div><div>rlist = 1.2</div><div>rcoulomb = 1.1</div><div>rvdw = 1.0</div><div>vdwtype = shift</div>
<div>rvdw-switch = 0.9</div><div>coulombtype = PME-Switch</div><div>Tcoupl = v-rescale</div><div>tau_t = 0.1 0.1</div><div>tc-grps = protein non-protein</div>
<div>ref_t = 300 300</div><div>Pcoupl = parrinello-rahman</div><div>Pcoupltype = isotropic</div><div>tau_p = 0.5</div><div>compressibility = 4.5e-5</div>
<div>ref_p = 1.0</div><div>gen_vel = yes</div><div>nstxout = 2 ; write coords every # step</div><div>lincs-iter = 2</div><div>DispCorr = EnerPres</div>
<div>optimize_fft = yes</div><div>EOF</div><div><br></div><div>grompp -f em.mdp -c Protein_b4ion.pdb -p Protein.top -o Protein_b4ion.tpr</div><div>\cp Protein.top Protein_ion.top</div><div><br></div><div>echo 13 | genion -s Protein_b4ion.tpr -o Protein_b4em.pdb -neutral -conc 0.15 -p Protein_ion.top -norandom</div>
<div><br></div><div>\mv Protein_ion.top Protein.top</div><div><br></div><div>grompp -f em.mdp -c Protein_b4em.pdb -p Protein.top -o em.tpr</div><div><br></div><div>mdrun -v -deffnm em</div><div><br></div><div>grompp -f md.mdp -c em.gro -p Protein.top -o md.tpr</div>
<div><br></div>And it fails for the command above with:</div><div><br></div><div><div>-------------------------------------------------------</div><div>Program grompp, VERSION 4.5-beta1</div><div>Source code file: inputrec.c, line: 161</div>
<div><br></div><div>Software inconsistency error:</div><div>Unknown epc value</div><div><br></div><div><br></div><div>Any ideas? Thanks,</div><div><br></div><div>Alan</div>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>
Department of Biochemistry, University of Cambridge. <br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>
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