[gmx-users] Embedding Protein into lipid bilayer

khourshaeishargh at mech.sharif.ir khourshaeishargh at mech.sharif.ir
Sun Feb 21 12:14:30 CET 2016

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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?

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

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

	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?

	Finally, I should again thank you because of your helps.

	best regards



	Ali khourshaei shargh (khourshaeishargh at mech.sharif.ir)

	Department of Mechanical Engineering

	Sharif University of Technology, Tehran, Iran

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 wouldnt be there, or to match some experimental data that used
the same form (as is actually the case here).

Dont choose "None" for termini unless you have constructed such
groups.  It
makes no physical or biological sense.  If you have a full-length protein,
will have normal termini.  Refer to any basic biochemistry text if you are
unfamiliar with what peptide bonds or protein termini are.



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




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