[gmx-users] Error with virtual sites

Ramon Crehuet ramon.crehuet at iqac.csic.es
Fri Apr 20 15:54:06 CEST 2018

Dear all, 

I am trying to setup the simulation of a system composed of several peptide chains in water, using Charmm27 FF in TIP3P water. All residues are standard and I've done similar protein preparations other times. This time, however, I've got the following error when calling grompp for the initial equilibration (the energy minimzation ran fine): 

In molecule type 'Protein_chain_A' Virtual site 3fad construction involves 
atom 5, which is a virtual site of equal or high complexity. This is not 

Is there a way to solve this problem? Could this be due to an initial configuration where the different chains are very close to each other? 



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