[gmx-users] Inserting protein in Bilayer
Justin A. Lemkul
jalemkul at vt.edu
Sun Oct 11 23:48:53 CEST 2009
sunny mishra wrote:
> Hi Justin,
> Thanks for the quick reply. I am also following the martini tutorial
> in order to do the CG simulations. Here are the following steps which
> I am doing. Please have a look at them.
> 1) Cleaned the 1SU4.pdb file and renamed it to 1SU4_clean.pdb
> 2) converted 1SU4_clean.pdb to its CG structure using awk script and
> named it to 1SU4_cleancg.pdb
> 3) Then created the sequence of 1SU4_clean.pdb file and also the .ssd files.
> 4) Then using the seq2itp script created the protein.itp file for 1SU4.
> 5) Now I don't understand after this point what should I do because I
> also have to include DSPC molecules. Where should I include them I
> mean at which step?
> When I make my .top file for the protein do I include DSPC molecules
> there or anywhere else? Please let me know
That's what my tutorial addresses :) Sorry it's inaccessible at the moment. In
short, you need to #include the relevant .itp file for the lipids, like would
any other component of the system (solvent, ions, etc). See Chapter 5 of the
manual, as well as:
> On Sun, Oct 11, 2009 at 4:30 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>> sunny mishra wrote:
>>> Hi All,
>>> I am working on the CG simulations of the proteins and lipid bilayers.
>>> I am confused of how to set up the whole system for simulations. I got
>>> the DSPC lipid bilayer from martini website and I have 1SU4.pdb file
>>> with me. I cleaned the .pdb file and now I want to include the 14 DSPC
>>> molecules in my .pdb file. I don't know if I am going in the right
>>> direction or not. Please let me know how to set up the simulation for
>>> the same if you have some idea. I will appreciate your help.
>> I wrote a tutorial for atomistic membrane protein systems:
>> It may provide some useful information, since the premise for constructing
>> the system is the same. Our web server is currently down due to a power
>> outage at our University, but I should have everything up and running by
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>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> gmx-users mailing list gmx-users at gromacs.org
>> Please search the archive at http://www.gromacs.org/search before posting!
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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