Dear all,<br><br>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. <br><br>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.<br>
<br>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:<br><br>Fatal error:<br>Atom CG not found in residue GLN82 while adding hydrogens<br>
<br>Then I tried all other force fields. Only the following didn't give that error:<br><br> 0: GROMOS96 43a1 force field <br> 1: GROMOS96 43a2 force field (improved alkane dihedrals)<br> 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)<br>
3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) <br> 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) <br> 6: [DEPRECATED] Gromacs force field (see manual)<br><br>Is any of them good enough? If not, is there any way (such as a good free software) to fill in the missing atoms?<br>
<br>Thanks a lot!<br><br>Peggy<br>