[gmx-users] Two questions when simulate the protein in lipd bilayer: 1. ratio of water/lipid; 2. ligand charge
spoel at xray.bmc.uu.se
Sat Jun 21 20:12:01 CEST 2003
On Fri, 2003-06-13 at 02:16, Jerry Song wrote:
> Hello, Dear gmx user,
> I have two questions: one for simulation of protein+lipid+solvent; the
> other for the atomic charge of small ligand.
> 1. Are there any requirement for the ratio of
> water/lipid when simulating the protein+lipid+solvent system?
> I tried to simulate a protein (GPCR) in equlibrated DPPC lipid layer
> (128 lipid and 3655 water, downloaded
> from Tieleman's webpage). After I inserted the protein into
> the bilayer and then add the solvent to keep protein
> around 0.5nm away from box edge ( in z direction). The whole system
> ended up with protein + 109 lipid + 5504 solvent
> (8 of them would be replaced by ion later). When I checked the
> references, the ratio of water/lipid are always around
> 20 - 30, however the ratio of water/lipid in my modeling system is
> about 50. Would this ratio in my case improper? If not,
> how about making a hole for protein in the lipid molecule only (delete
> the water from downlaod pre-equilibrated system) and
> then add the water later according to the proper ratio during the
> solvation step.
more water is better but more expensive. 3655 is still peanuts though.
> 2. the 2nd question is related with the topology generation of ligand
> (small molecule).
> Can I use PRODRUG server to generate the initial topology for ligand,
> replace the atomic charges with Chelpg charges,
> and then simulate the ligand in vacume or solvent box for
> validation. I saw some previous disccussion (for ligand) about
> the replacing Gromas96 charges. Would the same "side-effect", the
> requirement for the re-adjustment of other parameters
> (such as Lennard-Jones par.) , occur too? Or can I just use
> the RESP fitting to generate the AMBER topoly and then
> convert it into gromacs format using AMBCONV?
I'd say your protocol starting from prodrg is OK. Validation is
important but may be difficult... Going through AMber probably doesn't
> Thanks in advance
Dr. David van der Spoel, Dept. of Cell and Molecular Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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