[gmx-users] Embedding Protein into lipid bilayer

[Justin Lemkul]

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On 2/20/16 5:30 AM, khourshaeishargh at mech.sharif.ir wrote:
>
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>
> 	Hi Catarina
>
>
> 	Thanks for your reply, I really appreciate it. you know, I complete
> Justin&#39;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&#39;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&#39;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&#39;t make any chemical sense to use
> "None" for non-capped protein chains.
>
>
> 	I don&#39;t grasp what specifically Justin meant to say. Could anyone one
> please help me ? How should I naturalized the termini ?
>

The tutorial uses a modeled peptide fragment.  Typically fragments of larger 
proteins are capped with neutral groups to avoid artifacts of charged termini 
that normally wouldn't be there, or to match some experimental data that used 
the same form (as is actually the case here).

Don't choose "None" for termini unless you have constructed such groups.  It 
makes no physical or biological sense.  If you have a full-length protein, these 
will have normal termini.  Refer to any basic biochemistry text if you are 
unfamiliar with what peptide bonds or protein termini are.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================