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
- Used editconf to create translated copies
- 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?
You can use .pdb format just fine. There is no requirement that you use .gro,
and in fact the format specification of .gro does not include a field for chain
identifier, so no, there is no way to include chain identifiers in a .gro file.
-Justin
Thanks a lot,
Massimo
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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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