I can think of a few cholesterol topologies just off the top of my head:
GROMOS43A1-S3 forcefield has an entry for cholesterol
There is a stream file for cholesterol available for use with the CHARMM
forcefields.
There are other available too, you should use google to find them. I
have never used any of them so would not like to comment on which to
use, this is up to you to decide after a thorough read of the literature.
Cheers
Tom
#ZHAO LINA# wrote:
Hi,
Thanks for your answer, I will spend some time to figure it out.
By the way, any links or literature or something relevant to it warmly welcome
to introduce them to me.
Best regards,
lina
________________________________________
From: [email protected] [[email protected]] on behalf
of Justin A. Lemkul [[email protected]]
Sent: Friday, October 01, 2010 9:06 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] cholesterol
#ZHAO LINA# wrote:
Hi,
It will be so bad for me if it really does not exist.
I wish probably except asking Dr. google, someone else will be able to provide
me some links.
I once just wanted to see some examples how they handled its topology even I
got one from
PRODRG server, but it has problems later. Not so much in those specific
simulations yet, just beginning stage.
If your problem is with deriving parameters, then do a thorough literature
search. Simulations with cholesterol have been done with numerous force fields,
so parameterization methodology and/or suitable parameters should be available.
-Justin
lina
________________________________________
From: [email protected] [[email protected]] on behalf
of Justin A. Lemkul [[email protected]]
Sent: Friday, October 01, 2010 8:35 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] cholesterol
#ZHAO LINA# wrote:
Hi,
Are there some tutorials handling the cholesterol stuff. I read several
literature but choked in some places.
I said this to someone just the other day: if it's not linked at
http://www.gromacs.org/Documentation/Tutorials or you can't find it with Google,
it probably doesn't exist.
What's more, "handling the cholesterol stuff" doesn't really lend itself to
getting useful help. What are you trying to do? Derive parameters? Build a
membrane? A micelle? An LDL complex?
-Justin
Thanks with best regards,
lina
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Dr Thomas Piggot
University of Southampton, UK.
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