15 jun 2012 kl. 09.16 skrev Mark Abraham:

> 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 works.

It seems that some tools honor the chain IDs while some do not. I think trjconv 
is one of them, so Mark's suggestion would work in that caase. If not, then a 
combination of cut -b and paste on your new and old pdb would fix your problem.

Normally this is not a problem for simulation, but for quick visualization and 
inspection it's annoying.

Erik

> 
> Mark
> -- 
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-----------------------------------------------
Erik Marklund, PhD
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