Dear Jason,
When you assign syn- and anti- position to carboxylates do you specify it as dummy atoms (zero charge and zero VDWs) with coordinate positions in mol2 file ? I assigned same bond length O-H (0.96) and same angle between H-O-H (120).
C -3.3040 1.1729 -1.0796 C 0.520
O -2.4523 0.5812 -1.9611 O -0.440
O -2.8408 1.8405 0.0123 O -0.530
H -1.8963 1.9010 0.1730 H 0.450
H -1.7567 1.6750 0.1566 H 0.000
H -1.6838 0.9879 0.1524 H 0.000
H -1.7867 1.5643 0.1657 H 0.000
I can successfully generate the cpin file (explicit CpHMD). But when I use the new topology file generated with the Cpin file for minimization , it crashes with really high bond energy and EEL. What am I doing wrong ? I would really appreciate your help.
Thanks
NSTEP ENERGY RMS GMAX NAME NUMBER
1 2.3281E+11 3.6254E+03 8.6346E+04 H17 17
BOND = ************* ANGLE = 104927.7876 DIHED = 27.0368
VDWAALS = 2735.2308 EEL = -4649.9270 HBOND = 0.0000
1-4 VDW = 2881.3052 1-4 EEL = 23.8476 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
50 2.3279E+11 1.5984E+04 4.0015E+05 O 807
BOND = ************* ANGLE = 161204.8563 DIHED = 114.5431
VDWAALS = 191541.2503 EEL = -4494.1588 HBOND = 0.0000
1-4 VDW = -0.0764 1-4 EEL = 8.7276 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
100 2.3273E+11 1.3413E+04 4.2746E+05 C10 10
BOND = ************* ANGLE = 168394.1896 DIHED = 136.1485
VDWAALS = 101128.9772 EEL = -4532.7534 HBOND = 0.0000
1-4 VDW = -0.0020 1-4 EEL = 4.7006 RESTRAINT = 0.0000
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Received on Wed Sep 09 2015 - 08:30:03 PDT
