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

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jun 15 09:16:47 CEST 2012

On 15/06/2012 5:06 PM, Samuel Flores wrote:
> 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?

IIRC there has been list traffic about this in the past, if you search. 
Certainly grompp doesn't bother trying to retain chain IDs. editconf 
allows you to add chain IDs afterwards, but I have no idea if it lets 
you do it on a per-group basis. Another option might be taking the final 
frame in the trajectory and using it (-f) and your original .pdb file 
(-s) as input to trjconv to write a .pdb file, but I don't know if that 


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