VMD-L Mailing List

From: Chia-Ju Hsieh (chiahs_at_mail.med.upenn.edu)
Date: Thu Sep 15 2016 - 10:15:34 CDT

Hi,

I have a small molecular structure conformed as R-N3, and used CgenFF to parametrize the ligand. When I running NAMD simulation seems like it stop at somewhere regarding azide. The error information from the output file are shown in the end of the message.

Is this something wrong with the parameter and topology file?

Thanks,

Chiaju

Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Warning: DUPLICATE BOND ENTRY FOR NG1D1-NG1D1
PREVIOUS VALUES k=1244.39 x0=1.1395
   USING VALUES k=696.682 x0=1.2367
Warning: DUPLICATE ANGLE ENTRY FOR CG2R61-CG2R61-NG1D1
PREVIOUS VALUES k=42.252 theta0=116.2 k_ub=0 r_ub=0
   USING VALUES k=43.173 theta0=123.94 k_ub=0 r_ub=0
Warning: IDENTICAL PERIODICITY! REPLACING OLD VALUES BY:
  k=0.3794 n=2 delta=180
Warning: IDENTICAL PERIODICITY! REPLACING OLD VALUES BY:
  k=0.3824 n=2 delta=180
Warning: DUPLICATE DIHEDRAL ENTRY FOR CG2R61-CG2R61-CG2R61-NG1D1
PREVIOUS VALUES MULTIPLICITY: 1
  k=0.6104 n=2 delta=180
Warning: IDENTICAL PERIODICITY! REPLACING OLD VALUES BY:
  k=0.6519 n=2 delta=180
Warning: DUPLICATE DIHEDRAL ENTRY FOR HGR61-CG2R61-CG2R61-NG1D1
PREVIOUS VALUES MULTIPLICITY: 1
  k=0.6397 n=2 delta=180
Warning: IDENTICAL PERIODICITY! REPLACING OLD VALUES BY:
  k=0.6624 n=2 delta=180
FATAL ERROR: ABNORMAL EOF FOUND - buffer=*END*