[gmx-users] multi-chain pdbs with mdrun?

Samuel Flores samuelfloresc at gmail.com
Fri Jun 15 09:06:25 CEST 2012

HI Guys,

I'm trying to run a short equilibration of p56 tetramer in water.  I issue:

/home/flores/local/gromacs/bin/mdrun -v -deffnm em -c  /home/flores/projects/antibody-design/13JUN12/352/last.2.em.pdb

The problem is that last.2.em.pdb has four chains, but none have chain ID's!  The file I start with has chains A,B,C, and D, but gromacs seems to strip these and replace them all with " ".

Is there any easy way to prevent the chain ID's from being lost?  Or do I need to write a script to put them back in?


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