On 8/6/17 4:21 PM, 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; } Hi justin
Thank you for your replyingBut you said in this tuturial, in order to have tc_groups = protein non-protein , it is best to consider protein and ligand as one single entity. So we use make-ndx to merg them. When i issue
...for the purpose of thermostatting, nothing else. Again, merging two groups
doesn't eliminate either from the list unless you actually deleted them.
gmx hbond there isnt any ligand in this list to choose. How can i determine h
bonds between protein and ligan , even in my project that is about HDAC2 and my
designed drug
If you're working on a different system, you're not going to have the exact same
options as in my tutorial. Likely your ligand isn't called "JZ4," so look for
something else that makes sense for your system.
-Justin
Thank you Farial
Sent from Yahoo Mail for iPhone
On Sunday, August 6, 2017, 5:06 AM, Justin Lemkul <jalem...@vt.edu> wrote:
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
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
