Re: namd: DSPC and DAPC for a phospholipid bilayer

From: SMAHANE CHALABI (smahane_chalabi_at_hotmail.com)
Date: Fri Apr 20 2007 - 09:10:28 CDT

hi,

Thanks for your answer. I have no parameters for those molecules, but I will
support my study on experimental measurements, which validate it.
I have read that many MD simulations, which use DSPC and DAPC for
phospholipid bilayer, are done using GROMACS or CHARMM. If you have been
already confronted to a such problem, could you advice me?

Thanks.

Yours sincerely,
Smahane CHALABI

>From: Cesar Luis Avila <cavila_at_fbqf.unt.edu.ar>
>To: SMAHANE CHALABI <smahane_chalabi_at_hotmail.com>
>Subject: Re: namd-l: namd: DSPC and DAPC for a phospholipid bilayer
>Date: Fri, 20 Apr 2007 10:09:07 -0300
>
>Hi,
>do you already have the parameters for those molecules? Do you have any
>experimental measurement to validate your simulations? There are many
>papers already published on how to build, and equilibrate a membrane.
>Regards
>Cesar
>
>SMAHANE CHALABI escribió:
>>Hi,
>>
>>I am currently doing a training period within my Master of science and
>>Computational Biology at Evry, in France. This one consists in Molecular
>>modeling and drug design, and I will have to use Visual Molecular Dynamics
>>to simulate a membrane biologic. So, I’ll have to use unusual
>>phospholipids such as distearoylphosphatidylcholine (DSPC) and
>>diarachidoylphosphatidylcholine (DAPC).
>>
>>However, VMD version 1.8.6 is able to generate a phospholipid bilayer
>>composed by POPE or POPC as we can see in the text consol window such as:
>>
>>Usage: membrane -l <lipid> -x <xsize> -y <ysize> {-o <prefix>}
>><lipid> is lipid name (POPC or POPE; others as added)
>><xsize> and <ysize> are membrane sizes in X and Y (Angstroms)
>><prefix> is optional output file prefix (default "membrane").
>>
>>However, I don’t know how to construct the template box structures for
>>DAPC and DSPC. So, I would like to ask you if anybody has already been
>>confronted to a such problem.
>>I have seen that there is a combined CHARMM All-Hydrogen topology file for
>>proteins and lipids, which contains POPC and POPE topologies.
>>Would I have to create a topology file for DSPC and DAPC? and/or is there
>>an other way to construct this box structures?
>>
>>Thanks very much for your answers!!
>>
>>Yours sincerely,
>>Smahane CHALABI
>>
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>

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