[gmx-users] Bonds break while Minimising using distance restraints

plmallip at mail.uh.edu plmallip at mail.uh.edu
Mon Sep 1 23:59:26 CEST 2008

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
;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,

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