[gmx-users] How to fix four different atoms of diffrent residue in tetrahedral geometry while MD.

[Anil Kumar]

Hi,

I wnat to do MD of 16mer polypeptide with fixed  tetrahedral geometry of
four different atoms of four different residue.

I donot understand how to give distance restrain to fix these four atoms.

I tried dis_rest.itp

[distance_restraints file]
; ai    aj      type    index   type'   low     up1     up2     fac
22      61      1       0       1       0.310   0.335   0.345   1
22      109     1       1       1       0.310   0.335   0.345   1
22      148     1       1       1       0.310   0.335   0.345   1
61      109     1       1       1       0.310   0.335   0.345   1
61      148     1       1       1       0.310   0.335   0.345   1
109     148     1       1       1       0.310   0.335   0.345   1

I have included this in corresponding top file.

; Include Position restraint file
#ifdef DIS_REST
#include "dis_rest.itp"
#endif

But still it is not working. Can anyone help me !!
Should i have to include this in *.mdp file ?

Thanks in advance.
Regards,
anil


ANIL KUMAR(Research Scholar)
Bio-Organic Lab No-336(2nd Floor)
Dept. of Chemistry,
I.I.T.Bombay,Powai,
Mumbai-400076 (INDIA)
Ph. No.-022-25764780(Lab),
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Hostel#1,Room#297,IIT Bombay,Powai,
Mumbai-400076,Ph.No.:-022-56036275(Hostel),
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