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

[Daan van Aalten]

Hi Jerry

PRODRG now includes an algorithm which "distributes" formal charges over
atoms in the molecule according to their relative electronegativities.
On a test set of molecules, this approach gives an RMSD of (only) 0.1
electron compared to charges calculated on the same test set of molecules
with GAMESS.

However - it is important to ensure protonation is correct, you can
correct that with ADDHYD/DELHYD (see faq) commands *at the end* of your
input file.

cheers

Daan

On Thu, 12 Jun 2003, 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.
>
> 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
> Minghu
>


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Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

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