VMD-L Mailing List

From: Robin Betz (robin_at_robinbetz.com)
Date: Sat Mar 02 2019 - 23:15:39 CST

Hi Kelly,

Where did you obtain this PDB file? It's missing the element field and says
"AO1" for the elemnet for each atom instead. While elements can be inferred
by atom names as cgenff is doing, it's not reliable in general. VMD / FFTK
has no way of confidently knowing what each atom is. I'd guess that the
code that generates Gaussian input files renames atoms based on element to
ensure the names are unique.

As PDB file parsing can be tricky in general, I'd recommend carefully
checking any PDB files you input to other programs and make sure they
conform to the official specification:
http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM

HTH,
Robin

On Sat., Mar. 2, 2019, 9:03 p.m. McGuire, Kelly, <mcg05004_at_byui.edu> wrote:

> 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*
>
>
>