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<DIV><FONT face=Arial size=2>Hello, Dear gmx user,</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>I have two questions: one for simulation of
protein+lipid+solvent; the other for the atomic charge of small
ligand.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>1. Are there any requirement for the
ratio of water/lipid when simulating the protein+lipid+solvent
system? </FONT></DIV>
<DIV><FONT face=Arial size=2>I tried to simulate a protein (GPCR) in
equlibrated DPPC lipid layer (128 lipid and 3655 water, downloaded </FONT></DIV>
<DIV><FONT face=Arial size=2>from Tieleman's webpage). After I
inserted the protein into the bilayer and then add the solvent to
keep protein </FONT></DIV>
<DIV><FONT face=Arial size=2>around 0.5nm away from box edge ( in z
direction). The whole system ended up with protein + 109 lipid + 5504
solvent</FONT></DIV>
<DIV><FONT face=Arial size=2> (8 of them would be replaced by ion
later). </FONT><FONT face=Arial size=2> When I checked the
references, the ratio of water/lipid are always
around </FONT><FONT face=Arial size=2></FONT></DIV>
<DIV><FONT face=Arial size=2>20 - 30, however the ratio of water/lipid in
my modeling system is about 50. Would this ratio in my case
improper</FONT><FONT face=Arial size=2>? If not, </FONT></DIV>
<DIV><FONT face=Arial size=2>how about making a hole for protein in the lipid
molecule only (delete the water from downlaod pre-equilibrated system)
and</FONT></DIV>
<DIV><FONT face=Arial size=2> then add </FONT><FONT face=Arial size=2>the
water later according</FONT><FONT face=Arial size=2> to the
proper ratio during the solvation step</FONT><FONT face=Arial
size=2>. </FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>2. the 2nd question is related with the
topology generation of ligand (small molecule). </FONT></DIV>
<DIV><FONT face=Arial size=2>Can I use PRODRUG server to generate the
initial topology for ligand, replace the atomic charges with Chelpg
charges,</FONT></DIV>
<DIV><FONT face=Arial size=2> and then simulate the ligand in vacume
or solvent box for validation. I saw some previous disccussion (for
ligand) about</FONT></DIV>
<DIV><FONT face=Arial size=2> the replacing Gromas96 charges.
Would the same "side-effect", the requirement for the re-adjustment of
other parameters </FONT></DIV>
<DIV><FONT face=Arial size=2>(such as Lennard-Jones par.) , occur
too? Or can I just use the RESP fitting to generate the AMBER
topoly and then </FONT></DIV>
<DIV><FONT face=Arial size=2>convert it into gromacs format using
AMBCONV? </FONT> </DIV>
<DIV><FONT face=Arial size=2> </FONT></DIV>
<DIV>Thanks in advance</DIV>
<DIV>Minghu</DIV></BODY></HTML>