[gmx-users] Embedding Protein into lipid bilayer

Justin Lemkul jalemkul at vt.edu
Sun Feb 21 21:24:48 CET 2016

On 2/21/16 5:44 AM, khourshaeishargh at mech.sharif.ir wrote:
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> 	Dear Justin
> 	first of all, thanks for your replay. but I should cite that the bizarre
> character that you saw in my Email was Sharif university Email domains
> fault not me. also different copies of Email was because of the fact that
> I didnt know how to use gmx-user. from now on, I try not to bother my
> friends in gmx-user anymore.
> 	to be honest, I need to simulate a cell membrane with 1r2c protein and
> exert some tests like creep and compliance onto it to obtain viscoelastic
> response of it. after finishing your tutorial, I thought that now I can
> do it. I downloaded 1r2c pretin from PDB bank. but unfortunately at the
> beginning I confront with fatal error. I really appreciate it if you
> answer my below question.
> 	1. the PDB which we usually download from PDB bank is Full length not a
> peptide.isnt it?

Depends on the protein.

> 	2. Can I use the full length PDB file or I should change it to obtain a
> peptide?

Simulate whatever is relevant to your scientific question(s) at hand.  You do 
not need to conform to some simple tutorial example.  Tutorials are, by design, 
some small and reproducible system.  "Real" science is often much more complex.

> 	3. about the desired output I explained above, Can I obtain it based on
> the method you used in tutorial?

I don't really know what any of that is.  Use literature as your guide.  The 
tutorial is a simple how-to for setting up a heterogeneous system.  How you 
carry out and analyze the subsequent simulation depends entirely upon what you 
want to observe.

> 	4. If I use gmx pdb2gmx -f 1rc2.pdb -o 1rc2_processed.gro -ignh�
> -water spc, I mean without -ter, It says:
> 	Fatal error:
> 	There were 35 missing atoms in molecule Protein_chain_B, if you want to
> use this incomplete topology anyhow, use the option -missing
> 	can I keep on using -missing or not?

Absolutely not.  This will build an incomplete model that is physically 
unrealistic.  As a general rule, NEVER use -missing.  It is for niche cases 
only.  Check your input PDB structure for obvious MISSING entries that tell you 
about parts of the structure that were not resolved.  If these are internal 
residues, you need to build them using the appropriate modeling software (not 



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


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