[gmx-users] About -chainsep and -ter

[Justin A. Lemkul]

Hsin-Lin Chiang wrote:
> 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 ."

The -ter option allows you to change the protonation state of the termini.  The 
shorthand "iso" means "instead of," implying that charged termini are the 
default.  If you do not need to alter the protonation state of the termini, then 
you do not need the -ter option.

> 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.

Your system exploded because pdb2gmx likely tried to make your two chains one 
continuous protein, forming an unrealistic bond between the C-terminal of chain 
A and the N-terminal of chain B.  By removing the TER delimiter, you've 
essentially told pdb2gmx that you have one protein, not two.

> 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.

Assuming that the "y" response indicates that you want separate chains, that's 
why this approach works.  Regardless, if you have two distinct proteins (i.e. 
the backbones are not continuous), you do not want the chains to be considered 
continuous.  Disulfides are created in a separate mechanism utilizing 
specbond.dat and is independent of the use of -chainsep.

> They seems to the same in my two chain system.
> 

There is likely some difference (probably a single bond) that is causing the 
problem.

-Justin

> 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
> 
> 
> 
> 
>  
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================