[gmx-users] cholesterol

[#ZHAO LINA#]

Thanks for your clue.

I found the very interesting paper about that force field.

Thanks again,

lina


________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Thomas Piggot [t.piggot at soton.ac.uk]
Sent: Friday, October 01, 2010 9:22 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] cholesterol

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: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
> 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: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
>> 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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