[gmx-users] Embedding Protein into lipid bilayer

khourshaeishargh at mech.sharif.ir khourshaeishargh at mech.sharif.ir
Mon Feb 22 11:10:20 CET 2016

	Dear Justin

	Thanks for your reply. I think, I got what you mean. By the way, My
protein needs to use BGL residue and of course this type of the residue
isnt available in the gromacs sources. So I find its information in ATP
site and it is attached to my Email as a .itp file. I try to attach its
content to .rtp file  and add BGL to residuetype as protein to
gromos96 53a6, but again when I try to use pdb2gmx command, it fails and
says Residue BGL not found in residue topology database. also the
contents of the attached file isnt as same as the .rtp file writing. Any
Comment ? I really appreciate it.

	best regards



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

	Department of Mechanical Engineering

	Sharif University of Technology, Tehran, Iran

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

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