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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