Hi,:
Is it possible to solvate the system using coarse grained water
molecule?
I tried command: genbox -cp cg_protein.pdb -cs cgwat.pdb -o
cg_protein_water.pdb, but get Segmentation fault.
Can anyone give me some suggestion or basic procedure to build a
coarse grained system?
Thanks in advance.
Bin
On Nov 24, 2008, at 1:32 AM, Xavier Periole wrote:
On Sun, 23 Nov 2008 21:48:52 -0800
BIN ZHANG <[EMAIL PROTECTED]> wrote:
Hi, all:
Has anyone done the coarse graining using MARTINI force field?
Could you give me any suggestion on how to build a coarse grained
model from the AA system? I checked the website(http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html
) and it seems to me they only provide a script for coarse
graining peptide. My AA system will include protein+lipid+water.
The script indeed provides only transformation from AA to CG for
proteins.
It should be soon available for any AA system.
In the mean time you can do it with a script of your own, choosing the
atoms from your AA file.
XAvier
Thanks in advance.
Bin
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XAvier Periole - PhD
- Molecular Dynamics Group -
Computation and NMR
University of Groningen
The Netherlands
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