On 8/4/17 11:13 AM, farial tavakoli wrote:
  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear gromacs user
I am performing protein ligand complex (t4lysosim) and now i need to analyze JZ4 hydrogen bonding, 
but when i type Gmx hbondThere is no JZ4 in the list to choose. It is because of i used :Gmx 
make_ndx -f em.gro -o index.ndxAnd merged the " protein " and " JZ4" groupsIs 
there anyone help me how to check the hydrogen bond of JZ4 ligand?

Both protein and ligand are default groups and do not require the use of an index file. If the ligand isn't showing up in the list, it's probably because you're supplying an index file from which the ligand group has been deleted.



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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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