ms wrote:
Hi,
I am a gmx newbie, so please don't bite too much! :)
Learning gmx, I am experimenting with simulations with multiple
identical small chains. What I did was:
- I generated the peptides with pymol
- Generated a .gro with pdb2gmx
This step is "generating a molecular topology". You don't need a .gro -
it's just a regularized coordinate file produced as a side-effect.
- Used editconf to create translated copies
Try genconf to do the replication. That should remove much of the manual
labour. You would still probably need to edit in the chain IDs yourself,
but that's easy work with a script or good editor.
- Stitching them together and creating the complete file, adjusting
numbers etc. manually
It worked well, but the chains are not recognized as *different* chains
-which could be useful. Documentation says I should use another format
like the pdb, but it is a bit sparse on the subject. I think I can use
pdb instead of gro if needed, but does this also work when creating
boxes etc.? Isn't there a way to get chain identifiers in a gro file?
What is best practice?
What do you want the chain identifiers for? I'm not aware of a
post-pdb2gmx purpose that they might serve.
If your system is N identical peptides in a solvent, then best practice
for generating a complete .top is to generate one for a single peptide
in solvent (e.g. pdb2gmx - editconf - genbox). Then generate a
coordinate file which contains the N peptides' coordinates followed by
all the solvent (e.g. genconf - genbox). Then edit the [ molecules ]
section of the original .top to match. Other solutions are possible, but
require more involved use of pdb2gmx, and might indeed want chain IDs.
Mark
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