[gmx-users] POPC Membrane + protein dynamics

[padhu at ncbs.res.in]

Dear Justin,
Many thanks for your comprehensive mail. I will try to do it and let you
know if i come across any problem..(Definetely i may bug u again :))
Thank you so much.
Best regards
Padhu

>
>
> padhu at ncbs.res.in wrote:
>> Dear All,
>> I'm a new comer to gromacs. I need to perform molecular dynamics
>> simulation of my protein within the POPC membrane. I have downloaded the
>> 128a popc lipid from Prof.Tieleman's group along with the required
>> popc.itp. My protein of interest is 458 residues. Since the 128a popc is
>> already Simulated for 1600 ps, i haven't done membrane only simulation.
>> So
>> i directly aligned my protein with the membrane using VMD and have saved
>> the coordinates. However after i aligned my protein with the membrane, i
>> felt the membrane was not big enough for my protein of interest, also,
>> the
>> N-terminal region and the loop regions in the C-terminal region and
>> stretching outside water molecule above and below respectively.ow, i
>> have
>> two questions here...
>
> Yep, if the protein is sticking "out" of the box on both sides, the box is
> too
> small.
>
>> 1. How would i increase the number of lipids from the existing one?
>
> Two options:
>
> 1. genconf -nbox will give integer multiples of the lipid system (i.e.,
> -nbox 2
> 2 1 will expand the bilayer in the x and y directions and give 512 lipids)
>
> 2. genbox -cs popc128a.pdb -box (whatever dimensions) allows you a bit
> finer
> control over how large the box is and how many lipids will result.
>
>> 2. Also, i should increase increase the number of water molecules above
>> and below the membrane so that it covers the whole region of N-terminal
>> and also the loop regions of the C-terminal.
>
> Expand the box using editconf and add solvent with genbox.
>
>> Now, How to perform these tasks??If i do so will it be compatible with
>> the
>> popc.itp file which i downloaded from the Prof. Tieleman's group?
>>
>
> None of the above operations have any influence on the parameters
> contained in
> popc.itp.  If you are unsure about Gromacs workflows, file formats, etc.
> then
> you really need read the manual and do some more basic tutorial material
> before
> you attempt a difficult simulation like a membrane protein.  There are a
> lot of
> pitfalls in simulating such a complex system, and if you are not ready for
> them,
> then you can waste a whole lot of time generating nonsensical results :)
>
>> 3. My third question is while aligning my protein with the membrane
>> should
>> i make a hole first or after aligning the protein should i remove the
>> overlapping lipids with the proteins?which one would be better??
>>
>
> There are several methods for doing this.  See below.
>
>> I have tried out some of the methodologies available in the internet but
>> it dosen't help me.If anyone of you have a detailed step by step
>> methodology right from the first step to till running the MD simulation
>> please let me know.
>
> Saying you've tried things and they didn't work is useless.  What did you
> try?
> What links can you provide?  Have you tried the membrane protein tutorial
> linked
> from the Gromacs site?  That's about as step-by-step as it gets.
>
> -Justin
>
>> Your help will be highly appreciated.
>> Looking forward to hear from you.
>>
>> Best regards
>> Padmanabhan
>>
>
> --
> ========================================
>
> 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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