On 15/02/11 06:34, XAvier Periole wrote:
You have two problems:
1- the parameterization of phosphorylated serine should be done
following the same philosophy of Martini. Check the Martini papers
to see how this is done. In short partitioning is of primary importance.
2- you want to simulate unfol
regarding "parameterization of phosphorylated serine "
I checked the Martini papers and I couldn't find how it is done. Can
somebody please instruct me.
In addition in JCTC paper from 2008 I saw that they simulated
pentapeptides without imposing secondary structure. How can I do it?
The prob
one
+46 76 207 8763 Mobile
ran.fried...@lnu.se
http://lnu.se/ccbg
--
Message: 1
Date: Tue, 15 Feb 2011 00:43:51 +0200
From: pol...@fh.huji.ac.il
Subject: Re: [gmx-users] Simula
On Feb 14, 2011, at 11:43 PM, pol...@fh.huji.ac.il wrote:
Thank you very much for you reply. Can you please explain me why do
i need secondary structure file at all and why "secondary structure
is pre-defined and thus static throughout a simulation"? I didn't
see that something like this d
On Feb 14, 2011, at 7:24 PM, devicerandom wrote:
On 14/02/11 13:42, XAvier Periole wrote:
Dear Regina,
You have two problems:
1- the parameterization of phosphorylated serine should be done
following the same philosophy of Martini. Check the Martini papers
to see how this is done. In short p
Thank you very much for you reply. Can you please explain me why do i
need secondary structure file at all and why "secondary structure is
pre-defined and thus static throughout a simulation"? I didn't see
that something like this defined for lipids. How do I use do_dssp to
build the needed
On 14/02/11 13:42, XAvier Periole wrote:
Dear Regina,
You have two problems:
1- the parameterization of phosphorylated serine should be done
following the same philosophy of Martini. Check the Martini papers
to see how this is done. In short partitioning is of primary importance.
2- you want to
Dear Regina,
You have two problems:
1- the parameterization of phosphorylated serine should be done
following the same philosophy of Martini. Check the Martini papers
to see how this is done. In short partitioning is of primary importance.
2- you want to simulate unfolded protein ... indeed ther
Dear Gromacs users and developers,
I'm interested to run simulation of natively unstructured protein
(casein), that can self assembly and create micelles, using Martini
force field. The initial structure of the monomer was created and
minimized using Sybyl. This protein includes also 4 phosp
9 matches
Mail list logo
