Topic Options
#37205 - 12/04/18 04:56 AM How to get hbond Donor and Acceptor selection.
Rohit Offline
Forum Member

Registered: 10/25/17
Posts: 26
Hi,

I want to see the atoms in the donor and acceptor. How can i do that. Also I would like to remove all water from donor and acceptor and allow only protein atoms to be present in donor and acceptor.

I want to do atom selection such that only protein donor and acceptors are there in atom selection, how can i go about it.

Top
#37206 - 12/04/18 06:23 AM Re: How to get hbond Donor and Acceptor selection. [Re: Rohit]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4688
Loc: ~ 59N, 15E
coor hbond select .not. resn tip3 show end
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Top
#37208 - 12/05/18 01:17 AM Re: How to get hbond Donor and Acceptor selection. [Re: lennart]
Rohit Offline
Forum Member

Registered: 10/25/17
Posts: 26
I want just the selection.

Top
#37211 - 12/05/18 06:59 AM Re: How to get hbond Donor and Acceptor selection. [Re: Rohit]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4688
Loc: ~ 59N, 15E
What is your question?
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Top
#37217 - 12/06/18 02:02 PM Re: How to get hbond Donor and Acceptor selection. [Re: lennart]
Rohit Offline
Forum Member

Registered: 10/25/17
Posts: 26
I want the atoms in Donor and acceptors definition. so I can use it for other calculations.

Top
#37218 - 12/06/18 03:10 PM Re: How to get hbond Donor and Acceptor selection. [Re: Rohit]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8259
Loc: 39 03 48 N, 77 06 54 W
The definitions can be found in the topology files (RTFs).

The HBOND energy term in the CHARMM force field has been deprecated, and a number of the newer biopolymer files (e.g. lipid, carb) do not have DONOR or ACCE definitions. Those in prot or na seem okay, but I'm not sure about cgenff; some residues may have been missed, and there's too many to check quickly.
_________________________
Rick Venable
computational chemist


Top
#37220 - 12/06/18 04:07 PM Re: How to get hbond Donor and Acceptor selection. [Re: Rohit]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4688
Loc: ~ 59N, 15E
Just to be very specific: For the coor hbond command you shouldnot have to worry about donors and acceptors - coor hbond knows about this from the RTF.

Did you actually try the command I provided? Please do, it is
quite illustrative.

It is often the case that a little experimenting (formerly known as doing "science") helps you understand what is going on in a much better way, and more quickly, than just posting questions.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Top

Moderator:  John Legato, lennart