Dear colleagues,
I need to use simple distance restraints of 12.5 A between two CA atoms of two
residues. I am using the following lines in the .itp file
#ifdef DDISRES
[distance_restraints]
;ai aj type index type' low up1 up2 fac
1703 1712 1 0 1 11.5 12.0 12.5 1.0
The first feww line of .mdp file for minimisation of protein alone is
; Preprocessing
;
title = ${MOL}
cpp = /lib/cpp ;Preprocessor
define = -DDISRES ;For cg, and also steep
After minimisation, the restarined residues & the adjacent bonds
break. This results in fragmnets - residues alone, peptide bond alone and the
rest of the protein. The distance restrained residues seems to try to move
towards each other (6.04 A after minimisation) and this might have caused
fragmentation. I tried to use various upper and lower values for bond length so
as to increase flexibility. But, still I end up in the fragments.
Some of the suggestions in the archive says VMD doesn't show bonds if
they r above threshold value. When I checked the distances between the atoms,
one of them is really long CO-CA bond 3.23 A (normally its 1.59A). This means
the bond is no longer there.
I appreciate any suggestions in this regard.
Thanks & regards,
Latha.
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