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An easy way to build a protein in a bilayer is through the
charmm-gui website<br>
<a class="moz-txt-link-abbreviated" href="http://www.charmm-gui.org/">www.charmm-gui.org/</a><br>
Partial drawbacks are that you need CHARMM to perform final
equilibration <br>
and then may need to rename some atoms to work with GROMACS<br>
On plus side is that charmm36.ff retains the original CHARMM atom
names in the lipids<br>
Krzysztof Kuczera<br>
<br>
On 4/15/12 12:09 PM, Tomek Wlodarski wrote:
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cite="mid:CANAOJCtNE=VLMOwwxvC9DfZU=3sYE1W=Zs-cTTvMnxtOXg71NA@mail.gmail.com"
type="cite">
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Hi,
<br>
<br>
I would like to simulate protein in DMPC bilayer in Charmm36 ff.
<br>
I checked mailing list and KALP-15 tutorial, but still I have a
few basic questions.
<br>
<br>
1) I have problem with DMPC bilayer...
<br>
<br>
- VMD membrane builder only provides POPE and POPC lipids...
<br>
<br>
- on the Peter Tieleman page there is a pdb but with different
atom names and without H, of course I can rename atoms but pdb2gmx
would not regenerate hydrogens - lipids.hdb file is empty
<br>
<br>
- I have found also this page: <a moz-do-not-send="true"
href="http://terpconnect.umd.edu/%7Ejbklauda/research/download.html">http://terpconnect.umd.edu/~jbklauda/research/download.html</a>
and it works but I am not able to extend bilayer with genconf... I
always end up with separated copies of starting patch... even with
-dist 0 0 0.
<br>
<br>
2) How to choose proper lipid patch size and simulation box size?
For globular proteins I would just run editconf with -bt
dodecahedron -d 1. How it is done in membrane protein simulation?
<br>
<br>
<br>
Thanks a lot for any help and suggestions.
<br>
Best!
<br>
<br>
tomek
<br>
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<pre class="moz-signature" cols="72">--
Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: <a class="moz-txt-link-abbreviated" href="mailto:kkuczera@ku.edu">kkuczera@ku.edu</a>
<a class="moz-txt-link-freetext" href="http://oolung.chem.ku.edu/~kuczera/home.html">http://oolung.chem.ku.edu/~kuczera/home.html</a>
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