[gmx-users] Embedding Protein into lipid bilayer

[khourshaeishargh at mech.sharif.ir]

	Hi Catarina


	Thanks for your reply, I really appreciate it. you know, I complete
Justin's Tutorial, so I know what procedures I should do. but now I
want to embed 2rh1 protein into DPPC lipid bilayer  which I already
downloaded it from rcsb.com.  when I tried to use pdb2gmx  via
"gmx pdb2gmx -f 2rh1.pdb -o 2rh1_processed.gro -ignh -ter -water
spc", it says :


	

	 


	Select start terminus type for ASP-29

	 0: NH3+

	 1: NH2

	 2: None

	2

	Start terminus ASP-29: None

	Select end terminus type for LEU-342

	 0: COO-

	 1: COOH

	 2: None

	2

	End terminus LEU-342: None

	-------------------------------------------------------

	Program gmx, VERSION 5.0.5

	Source code file:
/home/ali/gromacs-5.0.5/src/gromacs/gmxpreprocess/pdb2top.cpp, line:
1091

	

	Fatal error:

	There is a dangling bond at at least one of the terminal ends. Fix your
coordinate file, add a new terminal database entry (.tdb), or select the
proper existing terminal entry.

	-------------------------------------------------------


	I found a similar question in which Justin replied it as below :


	You haven't added caps onto the input protein, you should expect to
get this error. In the tutorial, I build ACE and NH2 groups onto the
peptide to neutralize the termini. Since you haven't done this type
of modification, pdb2gmx will die because you have incomplete amides at
the ends of the chain. The "None" terminus instructs pdb2gmx to
not build additional H (in the case of NH2 or NH3+ termini) or O(H) (for
COO- and COOH). It doesn't make any chemical sense to use
"None" for non-capped protein chains.


	I don't grasp what specifically Justin meant to say. Could anyone one
please help me ? How should I naturalized the termini ?

best regards

Ali khourshaei shargh (khourshaeishargh at mech.sharif.ir)
Department of Mechanical Engineering
Sharif University of Technology, Tehran, Iran


	 


	 

You can also use g_membed (a GROMACS tool) for the protein insertion. In
the latest GROMACS versions g_membed is part of the mdrun tool (-membed
flag). The reference is Wolf_2010_JC
<http://onlinelibrary.wiley.com/doi/10.1002/jcc.21507/full>

g_membed is easily combined with LAMBADA as well.

On 19 February 2016 at 10:15, Catarina A. Carvalheda dos Santos <
c.a.c.dossantos
at dundee.ac.uk> wrote:

> Hi Ali,
>
> First create the topology for the protein alone using pdb2gmx.
>
> Then, and if you already have a pre-equilibrated membrane
patch, perform
> the protein alignment and insertion into the membrane. There
are several
> ways to do this (see below).
>
> Align the protein with the membrane:
> - manual procedure/visual inspection (not recommended)
> - based on OPM database information
> - automatic tools: CHARMM-GUI, CELLMICROCOSMOS or LAMBADA
>
> Insert the protein into the membrane:
> - Alchembed Jefferys_2015_JCTC
> <http://pubs.acs.org/doi/abs/10.1021/ct501111d>
> - CHARMM-GUI
> - CELLMICROCOSMOS
> - INFLATEGRO2Schmidt_2012_JCIM
> <http://pubs.acs.org/doi/abs/10.1021/ci3000453>
>
> I recommend the LAMBADA/INFLATEGRO2 combination.
>
> Keep in mind that automatic tools might fail, so you should
always check
> the output files at each step.
>
> After this, add the lipids to the topology file (number of
lipid molecules
> and lipid parameters) and proceed to solvation, adding ions,
minimization,
> equilibration and then production phase.
>
> I&#39;m not sure if this answers to your question, but I hope
it helps anyway.
>
> Cheers,
>
> On 19 February 2016 at 08:33, <khourshaeishargh
at mech.sharif.ir> wrote:
>
>>
>>
>>
>> Dear All
>> During researching Internet, I found justin and
Anirban&#39;s tutorial
>> about embedding protein
>> in lipid membrane. It was useful and I appreciate them but
I had one
>> question. as I understood, I should make some changes to
protein pdb file
>> ( 1r2h for Ex)
>>  before using it in  pdb2gmx command or the GROMACS
can&#39;t
>> keep on and will be died with a fatal error ( something
like adding cope
>> to the ends of the protein ). could
>> somebody please tell me what should I do ? by the way I
found out that
>> Justin&#39;s
>> tutorial do something with xleap amber on the pdb file.
>> Please tell me how specifically I should revise my protein
pdb file.
>>
>> best regards
>> Ali khourshaei shargh (khourshaeishargh
at mech.sharif.ir)
>> Department of Mechanical Engineering
>> Sharif University of Technology, Tehran, Iran
>>
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>
>
>
> --
> Catarina A. Carvalheda
>
> PhD Student
> Computational Biology Division
> SLS & SSE
> University of Dundee
> DD1 5EH, Dundee, Scotland, UK
>



-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
SLS & SSE
University of Dundee
DD1 5EH, Dundee, Scotland, UK