Dear all, I am new to MD simulation. I am trying to do an all-atom MD simulation with explicit water of a protein which has a few missing side-chain atoms of a GLN residue.
1. Which force field would you recommend? The protein is an x-ray crystal structure, about 200 residues. Hydrogen atoms and hydrogen bonding are important. 2. According to the Gromacs manual, OPLS is recommended for all-atom MD simulation. However, when I tried to use OPLS-AA as the force field, pdb2gmx returned me an error: Fatal error: Atom CG not found in residue GLN82 while adding hydrogens Then I tried all other force fields. Only the following didn't give that error: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 6: [DEPRECATED] Gromacs force field (see manual) Is any of them good enough? If not, is there any way (such as a good free software) to fill in the missing atoms? Thanks a lot! Peggy
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