I have some of the output file below: CHARMM> ! put the complex in a water box CHARMM> read sequ tip3 21173
CHARMM> gene wat1 noangle nodihe NO PATCHING WILL BE DONE ON THE FIRST RESIDUE NO PATCHING WILL BE DONE ON THE LAST RESIDUE GENPSF> Segment 2 has been generated. Its identifier is WAT1. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 2 Number of residues = 21745 Number of atoms = 72299 Number of groups = 23862 Number of bonds = 72427 Number of angles = 37194 Number of dihedrals = 23549 Number of impropers = 1535 Number of cross-terms = 570 Number of HB acceptors = 22035 Number of HB donors = 973 Number of NB exclusions = 0 Total charge = -17.00000 QXFORM> Expanded format used. More than 4 character RESID used.
Thanks,professor. But my crd file which produced together with this output file has many errors read by VMD as following. error> Base molecule :Excessive bonding errors encountered,perhaps atom coodinates are in the wrong units? error> Base molecule :Silencing bonding error messeges. <warning> Unusual bond between residues: 3 <protein> and 11251 <water> . . .
I am sure that my initial model before putting into the water box is minimized without error. I do not know what caused this.