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

[Samuel Flores]

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?

Sam

[Mark Abraham]

Post by Samuel Flores
HI Guys,
/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.

Mark

[Erik Marklund]

Post by Samuel Flores
HI Guys,
/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
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: [phone] fax: [phone]
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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