Dear rainy908,
If you compare the conformation generated by divcon/mopac/sqm/... or
even a QM program, the conformation obtained after geometry
optimization will never match that observed in experimental
conditions, and the differences will be huge... This, because of the
multiple negative charges of this molecule.
Thus, I do not think using the "whole molecule approach" is suitable
for this type of molecule. Instead you could use the building block
approach implement in R.E.D. or R.E.D. Server.
You will find GTP and far more cofactors in R.E.DD.B.
See
http://q4md-forcefieldtools.org/REDDB/projects/F-90/
vs
http://q4md-forcefieldtools.org/REDDB/projects/F-91/
You just run the "script1.ff" script in LEaP & you get all what you need...
http://q4md-forcefieldtools.org/REDDB/projects/F-90/script1.ff
http://q4md-forcefieldtools.org/REDDB/projects/F-91/script1.ff
regards, Francois
> I'm encountering the following error involving divcon when executing
> antechamber. I have no idea how to go about solving it. Can
> someone please help? thanks.
>
> $AMBERHOME/exe/antechamber -i frame0_desmond_3-out_gtp_h.ac -fi ac
> -o frame0_desmond_3-out_gtp_h.prepin -fo prepi -c bcc
[...]
> My input *.ac file is provided below:
> CHARGE 0.00 ( 0 )
> Formula: H14 C10 N5 O14 P3
> ATOM 1 PA GTP 1 -7.349 0.737 -0.920 0.000000 p5
> ATOM 2 O1A GTP 1 -8.784 1.425 -1.173 0.000000 o
> ATOM 3 O2A GTP 1 -7.073 -0.461 -1.763 0.000000 o
> ATOM 4 O5' GTP 1 -6.356 1.997 -1.121 0.000000 os
> ATOM 5 O3A GTP 1 -7.298 0.439 0.662 0.000000 os
> ATOM 6 PB GTP 1 -6.212 -0.588 1.301 0.000000 p5
> ATOM 7 O2B GTP 1 -4.831 -0.051 1.530 0.000000 oh
> ATOM 8 C5' GTP 1 -5.046 1.785 -1.602 0.000000 c3
> ATOM 9 C4' GTP 1 -5.056 1.546 -3.127 0.000000 c3
> ATOM 10 O1B GTP 1 -6.238 -1.789 0.201 0.000000 o
> ATOM 11 O3B GTP 1 -6.994 -1.268 2.572 0.000000 os
> ATOM 12 PG GTP 1 -7.371 -0.732 4.064 0.000000 p5
> ATOM 13 O2G GTP 1 -8.563 -1.722 4.509 0.000000 o
> ATOM 14 O3G GTP 1 -6.322 -0.659 5.115 0.000000 oh
> ATOM 15 O4' GTP 1 -5.936 2.519 -3.695 0.000000 os
> ATOM 16 C3' GTP 1 -3.677 1.828 -3.752 0.000000 c3
> ATOM 17 O3' GTP 1 -3.433 1.150 -4.973 0.000000 oh
> ATOM 18 C2' GTP 1 -3.747 3.310 -4.080 0.000000 c3
> ATOM 19 O1G GTP 1 -8.233 0.599 3.826 0.000000 o
> ATOM 20 O2' GTP 1 -2.918 3.643 -5.193 0.000000 oh
> ATOM 21 C1' GTP 1 -5.238 3.492 -4.385 0.000000 c3
> ATOM 22 N9 GTP 1 -5.672 4.827 -3.902 0.000000 na
> ATOM 23 C4 GTP 1 -5.335 6.028 -4.479 0.000000 cc
> ATOM 24 C5 GTP 1 -5.953 7.012 -3.736 0.000000 cd
> ATOM 25 C6 GTP 1 -5.779 8.387 -4.124 0.000000 c
> ATOM 26 N7 GTP 1 -6.668 6.433 -2.691 0.000000 nd
> ATOM 27 N1 GTP 1 -4.976 8.522 -5.258 0.000000 n
> ATOM 28 O6 GTP 1 -6.224 9.415 -3.617 0.000000 o
> ATOM 29 C8 GTP 1 -6.480 5.146 -2.834 0.000000 cc
> ATOM 30 C2 GTP 1 -4.398 7.460 -5.938 0.000000 cd
> ATOM 31 N2 GTP 1 -3.660 7.718 -7.019 0.000000 nh
> ATOM 32 N3 GTP 1 -4.535 6.200 -5.580 0.000000 nc
> ATOM 33 H5'1GTP 1 -4.465 2.666 -1.337 0.000000 h1
> ATOM 34 H5'2GTP 1 -4.592 0.936 -1.088 0.000000 h1
> ATOM 35 H4' GTP 1 -5.402 0.539 -3.362 0.000000 h1
> ATOM 36 H3' GTP 1 -2.861 1.599 -3.066 0.000000 h1
> ATOM 37 HO3 GTP 1 -2.980 1.810 -5.492 0.000000 ho
> ATOM 38 H2' GTP 1 -3.483 3.899 -3.200 0.000000 h1
> ATOM 39 HO2 GTP 1 -3.190 4.523 -5.439 0.000000 ho
> ATOM 40 H1' GTP 1 -5.498 3.452 -5.444 0.000000 h2
> ATOM 41 HN1 GTP 1 -4.862 9.480 -5.538 0.000000 hn
> ATOM 42 HN2 GTP 1 -3.277 6.929 -7.520 0.000000 hn
> ATOM 43 H9 GTP 1 -3.513 8.651 -7.366 0.000000 hn
> ATOM 44 H8 GTP 1 -6.918 4.396 -2.177 0.000000 h5
> ATOM 45 H7 GTP 1 -4.278 -0.739 1.908 0.000000 ho
> ATOM 46 H6 GTP 1 -6.706 -0.325 5.929 0.000000 ho
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Received on Thu Jan 26 2012 - 00:30:02 PST
