ms wrote:
Mark Abraham ha scritto:
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.
Very much right. Thanks.
- 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.
Thanks!
- 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.
This is where my naivety probably enters in: Analysis programs work on
groups. If several chains are defined, can each of these count as a
group? Indeed, chapter 8 doesn't explicitly say so, but... My intention
is to get analysis for each chain in my system. What is best practice
for that / where should I look in the docs?
make_ndx is the tool for generating such groups. If you read make_ndx -h
you'll see it does indeed let you create groups based around chain IDs,
but that'd (at least) require supplying it with a coordinate file that
has chain IDs. You could do that, but doing the house-keeping to assign
those IDs is tricky, and with PDB you're probably limited by 26 letters.
make_ndx will also let you create a group according to a range of atomic
numbers "a 1-10" or residue numbers "r 1-10". This avoids needing to
preserve/create chain IDs. Since you only need to create index groups
once for a given coordinate file, that's not too onerous. If you will
have lots of simulations with different numbers of such groups then you
might write a script to automate that... see
http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive
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.
Uh, thanks. Not sure to have understood all of it, but I will do my
homework before coming back :)
Sure. Doing some "irrelevant" tutorial material can be useful
introductions to the workflows. Regard;ess, the learning curve can be
steep for all computational chemistry software. Unfortunately no
beginner these days seems to want to come in and just do
protein-in-water :-) That makes their life hard.
Mark
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