[gmx-users] About -chainsep and -ter

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 21 19:15:41 CEST 2011

Hsin-Lin Chiang wrote:
>>I suspect this is a bug, so I have filed an issue on redmine:
>>In a previous issue (http://redmine.gromacs.org/issues/544), the "-chainsep 
>>interactive" option did not work, but now it does.  Conversely, "-chainsep ter" 
>>(which should also work in this case) does not.
> I get success in pdb2gmx, but I not only delete ter line but also all OXT lines according to this mailing list,
> http://www.mail-archive.com/gmx-users@gromacs.org/msg33251.html
> But I'm failed when I used mdrun in "-chainsep ter" case.

Right.  Even if you somehow force pdb2gmx to write a topology in this case, the 
bonds are not correct and the termini are incomplete.  That will hopefully be 
resolved when the bug is fixed.  For now, you have a workaround.  Just use 
"-chainsep interactive" and you will get a proper topology.



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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