I have prepared a system using leap that consist some organic molecule and a protein system.
The system has proper bonding as can be seen using VMD. After running minimisation steps, undesired bond form in organic molecules. I am using GAFF and ff99SB force fields.
No error may be seen in the leap log file.
Please suggest the reasons of this and the solutions.
Check the force field parameters for the organic molecules: atom types, bonds, angles, torsions, impropers, and partial atomic charges.
Martin Klvana
I have extracted the pdb file from RCSB PDB then added the missing atoms using a software and converted to mol2 format. Then, I have generated the frcmod file for the organic molecule using antechamber. After that, I have used the leap to generate the prmtop file for the parameters. Now, please suggest where should I cross check for the forcefield and parameters.
I think you should check in your forcefield file, is there any connections (bond, angle, dihedral angle) definition in your forcefield file (if yes, then this is your mistake when preparing forcefield).
If there is no mistake in forcefield preparation then it is OK because you just did Energy minimization, not physical dynamic, you should carry out some dynamic process in water like NVT/NPT equilibrium then check again.
VMD is just for visualization, it automatically adds a bond between two atoms if they are closed to each other
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