VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Sat Mar 02 2019 - 22:00:33 CST

  I ran this PDB through the CGENFF website, got a mol and str file, started at "Prepare Parameterization from CGenFF Program Output" under BuildPar tab, and I used those files to write a new PDB and PSF, which works throughout the rest of the FFTK process. I knew FFTK was sensitive to the PDB and PSF format, but it looks like you really need to get a new PDB and PSF through FFTK so that the atom names can be extracted for the Gaussian files.

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 7:55 PM
To: VMD Mailing LIst
Subject: vmd-l: Re: FFTK Possible Bug

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