[gmx-users] About -chainsep and -ter

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 21 13:37:16 CEST 2011

Hsin-Lin Chiang wrote:
> 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.

Please post a diff of the two topologies (the one that failed and the one that 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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