I am attaching here two files:
1. XXX_solv_ions.gro : This file was used for energy minimization and the residue (VAL 647) seems perfect here
2. em.gro : This file as obtained after energy minimization with gromacs 5.1.4 and amber99bsc1 force field. In this file, the residue VAL 647 seems to break. Dist bet CG1 and CB becomes greater than 3A.
Please let me know what could be the reason for the problem.
The script used for minimization is the simple one available for Lysozyme tutorial (Bevan Lab)
Hi. What type of bond is it?Some type of bonds are allowed to be broken. When performing energy minimization the goal is to equilibrate the internal forces between atoms. If the bond is for example of harmonic type, mathematically it will never break, but rather produce larger forces as the interatomic distance gets bigger. If u see a large distance this could mean that there are significant internal forces in equilibrium. One other possibility is that the minimization did not converge properly.
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