How to put distance restraints into topology file

User discussions
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24

Dear Magnus,
I am using dist rest just to keep atoms of my interest at correct distances;
i am not familier with NOE signalling thing;
I tried this:

; restraints for distances
[ intermolecular_interactions ]
[ distance_restraints ]
; ai aj type index type’ low up1 up2 fac
1610 4650 1 0 1 0.25 0.25 0.25 500
1624 4646 1 1 1 0.33 0.33 0.33 500
579 4646 1 2 1 0.33 0.33 0.33 500

and it gives error; when i comment two out of the three dist rest; it works; so simultaneous application is not working;
and this:

; restraints for distances
[ intermolecular_interactions ]
[ bonds ]
; ai aj type b0 kb
1610 4650 6 0.25 500
1624 4646 6 0.33 500
579 4646 6 0.33 500

i will try and let you know. Thank you for your generousity.

25

Magnus hi,
is this correct:
; restraints for angles
[ intermolecular_interactions ]
[ angle_restraints ]
;i j k l type theta fc multiplicity
1608 1610 4651 4645 1 180.0 2000 1
is this correct format; i want to restrain 1610 4651 4645 at 180 degrees.

26

Firstly, please avoid posting the same question in three different threads.

Regarding your question, I think it would work better with:

[ intermolecular_interactions ]
[ angles ]
;i j k type theta fc
1610 4651 4645 1 180.0 2000
27

Dear Magnus; thank you for your kind help; i will keep your words in mind, henceforth.

28

Dear Magnus,
when i try to simultaneously restrain angle of rxn and bond (distance) between the pair of atoms as:

[ intermolecular_interactions ]
[ angles ]
;i j k type theta fc
1610 4651 4645 1 180.0 2000

;[ intermolecular_interactions ]
[ bonds ]
; ai aj type b0 kb
1610 4651 1 0.25 2000

i get the following error:
Fatal error:
The intermolecular_interaction can not contain chemically bonding interactions

The atoms mentioned in the bonded interactions are not actually bonded;
1610 is protein atom, 4651 & 4645 are the ligand atoms;
what do you suggest how do i apply simultaneous restraints, over angle and bond (distance), explicitly.

29

As I wrote above (How to put distance restraints into topology file - #23 by MagnusL), you need a harmonic potential (type 6 bond):

[ intermolecular_interactions ]
[ bonds ]
; ai aj type b0 kb
1610 4651 6 0.25 2000

[ angles ]
;i j k type theta fc
1610 4651 4645 1 180.0 2000