[gmx-users] About -chainsep and -ter

Hsin-Lin Chiang jiangsl at phys.sinica.edu.tw
Thu Jul 21 08:19:36 CEST 2011

於 2011/7/21 上午 03:19, gmx-users-request at gromacs.org 提到:
>> 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.
Thanks for the explain.
>> >  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.
If I don't use -chainsep ter, then pdb2gmx will consider two chains as 
Protein-A and Protein-B.
The inter-disulfide bonds between two-chains will be lost.
>> >  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.
The question is ,
Merge chain ending with residue ASN21 (chain id 'A', atom 163OXT) with 
chain starting with
residue PHE1 (chain id 'B', atom 165 N)? [n/y]

Then I choose y, I think it's the same as -chainsep ter. Isn' it?
But for -chainsep ter, there is errors in mdrun.
For -chainsep interactive and type "y", everything correct.
>> >  They seems to the same in my two chain system.
>> >  
> There is likely some difference (probably a single bond) that is causing the
> problem.

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