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