[gmx-users] Imposing distance restraints between two residues

[plmallip at mail.uh.edu]

Dear colleagues,



           
I want to impose simple distance constraint between the two ends of the
same protein with missing residues in between. As I went through the
manual I found I can use "constraints type 2" fixes the distance without connecting atoms by a chemical bond.




Manual shows this example for O-H and H-H distances



[ settles ]

; OW funct doh dhh

1 1 0.1 0.16333

[ exclusions ]

1 2 3

2 1 3

3 1 2 
How can I do this for e.g. between two CA of the residues. Also, do you
suggest SHAKE or LINCS for this purpose? If you can give an example for
residues, just like the one above for water, that would be great.
Thanks in advance for any kind of suggestion in this regard.






warm regards,

Prema,

Graduate student,

UOH.


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