[gmx-users] Two questions when simulate the protein in lipd bilayer: 1. ratio of water/lipid; 2. ligand charge

Jerry Song songm at rpi.edu
Fri Jun 13 02:20:01 CEST 2003

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.   

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?       
Thanks in advance
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20030613/f829e9ab/attachment.html>

More information about the gromacs.org_gmx-users mailing list