Dear Mohammad,.
In Ambertools 18 we have included a set of TCL code which enables the embedding of proteins into lipid bilayers. The code is AMBAT, there are some example scripts included so that you can learn how to use it.
HTH
Ian
Tyrell: I'm surprised you didn't come here sooner.
Roy: It's not an easy thing to meet your maker.
Tyrell: What could he do for you?
Roy: Can the maker repair what he makes?
Bladerunner
--
Professor Ian R Gould, FRSC.
Professor of Computational Chemical Biology
Department of Chemistry
Imperial College London
Exhibition Road
London
SW7 2AY
E-mail i.gould.imperial.ac.uk
http://www3.imperial.ac.uk/people/i.gould
Tel +44 (0)207 594 5809
On 29/04/2018, 01:18, "Stephan Schott" <schottve.hhu.de> wrote:
Hi Mohammad,
In AMBER the lipids are separated in tails and heads independently (but
still linked through the forcefield). You can see a beter explanation of
this on the tutorial (
http://ambermd.org/tutorials/advanced/tutorial16/, a
bit outdated, but the main idea is there). For transforming your files into
AMBER you should use charmmlipid2amber.py (depending on the version, it
could also be called charmmlipid2amber.x). What version of AMBER are you
using? In the latest release (AmberTools18) there is a new script that
should do the work for you called packmol-memgen.
Cheers,
2018-04-29 0:29 GMT+02:00 Mohammad Salem <mohammad.alaraby.gmail.com>:
> Hi AMBER users,
>
> I tried to embed a protein in a POPC lipid bilayer using VMD. The
> generated pdb is unrecognised by amber. It has weird atom names that are
> not present in the lipid forcefield file or its extension.
>
> A sample is here:
>
> ATOM 1 N POPCL 1 -33.304 -39.250 20.920 1.00 0.00
> L11 N
> ATOM 2 C12 POPCL 1 -32.577 -38.468 22.038 1.00 0.00
> L11 C
> ATOM 3 H12A POPCL 1 -31.812 -37.824 21.442 1.00 0.00
> L11 H
> ATOM 4 H12B POPCL 1 -32.055 -39.156 22.715 1.00 0.00
> L11 H
> ATOM 5 C13 POPCL 1 -33.428 -38.491 19.695 1.00 0.00
> L11 C
> ATOM 6 H13A POPCL 1 -32.514 -37.985 19.477 1.00 0.00
> L11 H
>
> same for the water and ions.
>
> Is there a trick to convert the file to an AMBER-friendly format?
>
> Regards,
>
> Mohammad
>
>
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>
--
Stephan Schott Verdugo
Biochemist
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
Germany
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Received on Sun Apr 29 2018 - 02:30:02 PDT
