<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div>Dear GROMACS users,</div><div>I have been trying to set up a simulation system containing 4 Hypericin molecules in a box of water.</div><div>When I'm trying to run energy minimization,I get this error: </div><div><br></div><div>WARNING 1 [file HYP1_GMX.itp, line 5]:<br> Overriding atomtype CT<br><br><br>WARNING 2 [file HYP1_GMX.itp, line 6]:<br> Overriding atomtype CA<br><br><br>WARNING 3 [file HYP1_GMX.itp, line 7]:<br> Overriding atomtype C<br><br><br>WARNING 4 [file HYP1_GMX.itp, line 8]:<br> Overriding atomtype O<br><br><br>WARNING 5 [file HYP1_GMX.itp, line 9]:<br> Overriding atomtype OH<br><br><br>WARNING 6 [file HYP1_GMX.itp, line 10]:<br> Overriding atomtype HA<br><br><br>WARNING 7 [file HYP1_GMX.itp, line 11]:<br> Overriding atomtype
HO<br><br><br>WARNING 8 [file HYP1_GMX.itp, line 12]:<br> Overriding atomtype HC<br><br>Generated 2211 of the 2211 non-bonded parameter combinations<br>Generating 1-4 interactions: fudge = 0.5<br>Generated 2211 of the 2211 1-4 parameter combinations<br>Excluding 3 bonded neighbours molecule type 'HYP1'<br>Excluding 2 bonded neighbours molecule type 'SOL'<br>Analysing residue names:<br>There are: 4 Protein residues<br>There are: 5720 Water residues<br>Analysing Protein...<br>Number of degrees of freedom in T-Coupling group rest is 52125.00<br>Largest charge group radii for Van der Waals: 0.039, 0.039 nm<br>Largest charge group radii for Coulomb: 0.084, 0.084 nm<br>Calculating fourier grid dimensions for X Y Z<br>Using a fourier grid of 54x54x54, spacing 0.113 0.113 0.113<br>Estimate for the relative computational load of the PME mesh
part: 0.32<br>This run will generate roughly 6 Mb of data<br><br>There were 8 warnings</div><div><br></div><div>I generated the topology file using acpype,after that with BallView copied the hypericin molecules 4 times and saved to a pdb file.</div><div>In the topology file I made changes so that in [molecules] part,HYP1 was 4 (nmols) and for forcefield I included 1. #include "amber99sb.ff/forcefield.itp" , 2.#include "HYP1_GMX.itp" and then #include "amber99sb.ff/tip3p.itp".</div><div>I didn't have any problems with setting up the system with one molecule of Hypericin and water box.So what was my mistake?</div><div>I need your help<br></div><div>Thanks in advance<br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br><br></div></div></body></html>