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?
They can, but you have to define them. If there are multiple protein chains in
the system, the Gromacs tools will define them as one group - 'Protein' - and
not distinguish between them. This is a rather easy problem to solve, though,
without even using chain identifiers. You can create index groups based on
residue numbers to define each chain, then it doesn't matter what format the
coordinate file is in. For example, you can define groups like:
r 1-37
r 38-299
etc.
-Justin
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 :)
m.
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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