VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Sat Mar 02 2019 - 20:55:31 CST

Here is my starting PDB:

REMARK original generated coordinate pdb file
ATOM 1 C8 AMT A 1 0.259 -1.519 0.160 1.00 0.00 AO1
ATOM 2 C9 AMT A 1 0.994 -0.759 1.286 1.00 0.00 AO1
ATOM 3 H12 AMT A 1 2.091 -0.934 1.235 1.00 0.00 AO1
ATOM 4 H13 AMT A 1 0.632 -1.081 2.286 1.00 0.00 AO1
ATOM 5 C2 AMT A 1 0.735 0.757 1.138 1.00 0.00 AO1
ATOM 6 C3 AMT A 1 1.254 1.232 -0.236 1.00 0.00 AO1
ATOM 7 H3 AMT A 1 1.262 1.313 1.945 1.00 0.00 AO1
ATOM 8 H5 AMT A 1 2.349 1.063 -0.310 1.00 0.00 AO1
ATOM 9 H4 AMT A 1 1.071 2.323 -0.345 1.00 0.00 AO1
ATOM 10 C4 AMT A 1 0.523 0.473 -1.365 1.00 0.00 AO1
ATOM 11 C10 AMT A 1 0.782 -1.043 -1.213 1.00 0.00 AO1
ATOM 12 H6 AMT A 1 0.897 0.825 -2.352 1.00 0.00 AO1
ATOM 13 H14 AMT A 1 0.265 -1.572 -2.042 1.00 0.00 AO1
ATOM 14 H15 AMT A 1 1.875 -1.223 -1.307 1.00 0.00 AO1
ATOM 15 C5 AMT A 1 -0.992 0.745 -1.261 1.00 0.00 AO1
ATOM 16 C6 AMT A 1 -1.520 0.268 0.108 1.00 0.00 AO1
ATOM 17 H8 AMT A 1 -1.530 0.222 -2.080 1.00 0.00 AO1
ATOM 18 H7 AMT A 1 -1.182 1.835 -1.373 1.00 0.00 AO1
ATOM 19 H9 AMT A 1 -2.612 0.473 0.178 1.00 0.00 AO1
ATOM 20 C1 AMT A 1 -0.781 1.028 1.230 1.00 0.00 AO1
ATOM 21 H2 AMT A 1 -0.970 2.118 1.126 1.00 0.00 AO1
ATOM 22 H1 AMT A 1 -1.165 0.711 2.223 1.00 0.00 AO1
ATOM 23 C7 AMT A 1 -1.258 -1.247 0.258 1.00 0.00 AO1
ATOM 24 H10 AMT A 1 -1.659 -1.577 1.241 1.00 0.00 AO1
ATOM 25 H11 AMT A 1 -1.811 -1.780 -0.546 1.00 0.00 AO1
ATOM 26 N AMT A 1 0.507 -2.965 0.303 1.00 0.00 AO1
ATOM 27 H18 AMT A 1 0.153 -3.276 1.227 1.00 0.00 AO1
ATOM 28 H16 AMT A 1 1.528 -3.138 0.236 1.00 0.00 AO1
ATOM 29 H17 AMT A 1 0.010 -3.467 -0.457 1.00 0.00 AO1

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of McGuire, Kelly <mcg05004_at_byui.edu>
Sent: Saturday, March 2, 2019 7:28 PM
To: VMD Mailing LIst
Subject: vmd-l: FFTK Possible Bug

For the Windows 32 bit VMD 1.9.3 OpenGL version, when I generate Gaussian files from the PDB files (optimize geometry and water interaction tabs), the Gaussian files place X's instead of the atom name, which means Gaussian won't run. Is this a bug? Here is one of my Gaussian generated files:

%chk=AMT-ACC-H1.chk
%nproc=24
%mem=64GB
# HF/6-31G* Opt=(Z-matrix,MaxCycles=100) Geom=PrintInputOrient

<qmtool> simtype="Geometry optimization" </qmtool>
AMT-ACC-H1

1 1
X1 0.24899999797344208 -1.4600000381469727 0.15399999916553497
X2 0.9869999885559082 -0.7409999966621399 1.2790000438690186
X3 2.065999984741211 -0.9480000138282776 1.2209999561309814
X4 0.6290000081062317 -1.0920000076293945 2.256999969482422
X5 0.7260000109672546 0.7680000066757202 1.1260000467300415
X6 1.25 1.2369999885559082 -0.2370000034570694
X7 1.253999948501587 1.2940000295639038 1.930999994277954
X8 2.3329999446868896 1.0700000524520874 -0.3100000023841858
X9 1.0880000591278076 2.315999984741211 -0.3449999988079071
X10 0.515999972820282 0.4869999885559082 -1.3550000190734863
X11 0.7760000228881836 -1.0230000019073486 -1.2089999914169312
X12 0.8920000195503235 0.8100000023841858 -2.3329999446868896
X13 0.2669999897480011 -1.5759999752044678 -2.010999917984009
X14 1.8530000448226929 -1.2319999933242798 -1.2869999408721924
X15 -0.9919999837875366 0.7509999871253967 -1.2599999904632568
X16 -1.5110000371932983 0.2840000092983246 0.10599999874830246
X17 -1.5240000486373901 0.23399999737739563 -2.069000005722046
X18 -1.1890000104904175 1.8220000267028809 -1.3849999904632568
X19 -2.5899999141693115 0.460999995470047 0.1770000010728836
X20 -0.781000018119812 1.0329999923706055 1.2269999980926514
X21 -0.9750000238418579 2.1089999675750732 1.1419999599456787
X22 -1.1610000133514404 0.718999981880188 2.2079999446868896
X23 -1.2549999952316284 -1.2269999980926514 0.2549999952316284
X24 -1.6319999694824219 -1.5820000171661377 1.225000023841858
X25 -1.781999945640564 -1.781999945640564 -0.5339999794960022
X26 0.5059999823570251 -2.9570000171661377 0.3019999861717224
X27 0.16699999570846558 -3.305999994277954 1.2100000381469727
X28 1.5119999647140503 -3.1710000038146973 0.2409999966621399
X29 0.027000000700354576 -3.492000102996826 -0.4359999895095825
H1w X22 rAH X21 143.41 X20 180.00
  x H1w 1.0 X22 90.00 X21 0.00
 Ow H1w 0.9527 x 90.00 X22 180.00
H2w Ow 0.9527 H1w 104.52 x dih

rAH 2.0
dih 0.0

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602