VMD-L Mailing List

From: Ern Ong (Ern.Ong_at_student.adfa.edu.au)
Date: Sat Jan 20 2018 - 07:09:26 CST

Hi VMD users,

I encountered error terminations at Gaussian09 for 2 out of 12 HB acceptors and 3 out of 13 HB donors. The Gaussian input files for water interaction were generated using the default settings: # HF/6-31G* Opt=(Z-matrix,MaxCycles=100) Geom=PrintInputOrient (VMD1.9.3 2016-11-30 Windows platform). My molecule of interest is a single negatively charged mannose with a pyruvic acid group. The following is the summary of error messages:

#1 HB acceptor:
         Item Value Threshold Converged?
Maximum Force 0.000698 0.000450 NO
 RMS Force 0.000493 0.000300 NO
 Maximum Displacement 0.000349 0.001800 YES
RMS Displacement 0.000247 0.001200 YES
Predicted change in Energy=-2.434687D-07
Optimization stopped.
    -- Number of steps exceeded, NStep= 100
    -- Flag reset to prevent archiving.
Error termination request processed by link 9999.

#2 HB acceptor:
         Item Value Threshold Converged?
Maximum Force 0.000650 0.000450 NO
 RMS Force 0.000461 0.000300 NO
 Maximum Displacement 0.004805 0.001800 NO
 RMS Displacement 0.003399 0.001200 NO
 Predicted change in Energy=-1.559172D-06
Optimization stopped.
    -- Number of steps exceeded, NStep= 100
    -- Flag reset to prevent archiving.
Error termination request processed by link 9999.

#1 HB donor: (This water molecule is "spinning and flying" away from the very beginning)
         Item Value Threshold Converged?
Maximum Force 0.000058 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 1.403879 0.001800 NO
 RMS Displacement 1.011110 0.001200 NO
 Predicted change in Energy=-2.495560D-05
Optimization stopped.
    -- Number of steps exceeded, NStep= 100
    -- Flag reset to prevent archiving.
Error termination request processed by link 9999.

#2 HB donor: (This water molecule is also "spinning and flying" away from the very beginning)
         Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000009 0.000300 YES
Maximum Displacement 0.489277 0.001800 NO
 RMS Displacement 0.424264 0.001200 NO
 Predicted change in Energy=-2.355976D-05
Optimization stopped.
    -- Number of steps exceeded, NStep= 100
    -- Flag reset to prevent archiving.
Error termination request processed by link 9999.

#3 HB donor: (Since the water molecule is automatically assigned linearly at a 2 angstrom distance, the water molecule is found to be overly close to other atoms)
Small interatomic distances encountered: 33 29
Problem with the distance matrix.
Error termination via Lnk1e in

Hope that someone can help me solving the problems. I am not sure with the accuracy of charge optimization if I omit these water molecules, since I do not wish to further optimize the charges of atoms that these water molecules interact with.

Thank you.

Best Regards,

Ernest Ong Ern Seang

PhD student
School of Engineering and Information Technology (SEIT)
University of New South Wales@ ADFA
NorthCott Drive, Campbell
ACT 2600, Australia.