[gmx-users] About -chainsep and -ter

[Hsin-Lin Chiang]

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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