Hi everyone, My pdb file is consist of  two chains with one intra- two inter-disulfide bonds. So I used pdb2gmx in this way pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q -chainsep ter (I have deleted the TER and OXT lines of A-chain.) I'm not sure if I need to use -ter here, I don't understand the meaning of "interective termini selection, iso charged ." Anyway, I met problem after editconf, genbox, grompp, genion, and grompp. When I execute mdrun, I got the warning and terminated. Please see the long message below my name. However, if I used pdb2gmx in this way pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q -chainsep interactive  and selected y. Then everything is OK in mdrun step. I don't know what the different in -chainsep interactive and -chainsep ter is in my case. They seems to the same in my two chain system.
Sincerely yours, Hsin-Lin ------------------------------------------------- starting mdrun 'Protein in water' 7500000 steps,  15000.0 ps. Warning: 1-4 interaction between 196 and 207 at distance 3.231 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Step 0, time 0 (ps)  LINCS WARNING relative constraint deviation after LINCS: rms 66.078426, max 708.612183 (between atoms 207 and 208) bonds that rotated more than 30 degrees:  atom 1 atom 2  angle  previous, current, constraint length     207    208   90.0    0.1000  70.9612      0.1000 Back Off! I just backed up step0b.pdb to ./#step0b.pdb.4# Back Off! I just backed up step0c.pdb to ./#step0c.pdb.4# Wrote pdb files with previous and current coordinates Step 1, time 0.002 (ps)  LINCS WARNING relative constraint deviation after LINCS: rms 67071649.681650, max 719263296.000000 (between atoms 207 and 208) bonds that rotated more than 30 degrees:  atom 1 atom 2  angle  previous, current, constraint length     207    208   90.0   70.9612 71926328.0000      0.1000     212    213   90.0    0.1090   0.1308      0.1090     216    217   40.3    0.1090   0.1090      0.1090     218    219   90.0    0.1090   0.1545      0.1090     224    225   90.0    0.1000   0.3996      0.1000     232    233   90.0    0.1000   0.3867      0.1000     238    239   90.0    0.1000   0.1782      0.1000     238    240   90.0    0.1000   1.0652      0.1000     243    244   90.0    0.1000   0.3092      0.1000     250    251   90.0    0.1000   0.3082      0.1000     250    252   90.0    0.1000   0.2102      0.1000 step 1: Water molecule starting at atom 10744 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step1b.pdb to ./#step1b.pdb.4# Back Off! I just backed up step1c.pdb to ./#step1c.pdb.4# Wrote pdb files with previous and current coordinates Segmentation fault  
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