VMD-L Mailing List

From: Ghazaleh Zamani Maimian (ghazalehz_at_zedat.fu-berlin.de)
Date: Fri Nov 25 2016 - 03:25:42 CST

Dear VMD-L members

I am using fftk to parametrize my small molecule which is thioacetic acid
dimer with 16 atoms in total. I proceeded step by step, but while water
interaction optimization, two of the ~.gau files can not be optimized
using gaussian, while the rest are optimized properly. I get an error
"segmentation fault" and at the end of the log file:‌small interatomic
distances encountered: 20 3
would you please tell me what I can do to fix it?
I copy one of those ~.gau files here:

%chk=LIG-DON-HO2.chk
%nproc=4
%mem=4GB
# HF/6-31G* Opt=(Z-matrix,MaxCycles=100) Geom=PrintInputOrient

<qmtool> simtype="Geometry optimization" </qmtool>
LIG-DON-HO2

0 1
C1 0.30000001192092896 0.00800000037997961 -0.003000000026077032
C2 -0.057999998331069946 -0.013000000268220901 1.4529999494552612
S3 1.0440000295639038 -0.1589999943971634 2.6659998893737793
O4 -1.371999979019165 0.10300000011920929 1.6109999418258667
C5 -1.9620000123977661 -0.0560000017285347 7.23799991607666
H6 1.375 -0.0860000029206276 -0.14100000262260437
H7 -0.2160000056028366 -0.8130000233650208 -0.5099999904632568
H8 -0.05400000140070915 0.9440000057220459 -0.4449999928474426
C9 -1.6030000448226929 -0.032999999821186066 5.7820000648498535
O10 -0.28999999165534973 -0.1459999978542328 5.625
S11 -2.7049999237060547 0.1120000034570694 4.568999767303467
H12 -0.05251781642436981 -0.15160566568374634 4.71804666519165
H13 -1.6180000305175781 0.08900000154972076 2.5759999752044678
H14 -1.4470000267028809 0.7649999856948853 7.745999813079834
H15 -1.6080000400543213 -0.9919999837875366 7.678999900817871
H16 -3.0380001068115234 0.03700000047683716 7.375999927520752
  x H12 1.0 O10 90.00 C9 dih
 Ow H12 rAH x 90.00 O10 180.00
H1w Ow 0.9572 H12 127.74 x 0.00
H2w Ow 0.9572 H12 127.74 x 180.00

rAH 2.0
dih 0.0

Thanks in advance
Ghazaleh