[gmx-users] lipid problem
kolinkolin at poczta.onet.pl
Wed Nov 3 23:14:40 CET 2004
I just started learning gromacs. I need to simulate a GPCR in a lipid membrane.
I did all the examples at your site, but still have a problem:
At first I want to try simulating rhodopsin in a membrane.
- I have one pdb file with rhodopsin and some lipids and water after a MD simulation in NAMD (so all the coordinates are there) (I want to try it as a example)
- I did the topology file and coordinate file for the protein separately.
- I did the topology file for one lipid separately and every thing seems fine. (prodrg)
- I did coordinate file for one lipid separately. (prodrg)
My question is:
How can I combine protein and lipids and generate one *.gro (coordinate file) for my whole system.
How can I use my pdb file where I got all the coordinates for the system.
Should I treat every lipid as a separate molecule or as a solvent.
I would appreciate if you could give me some suggestions what should I do next. Thank you in advance.
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