Hi,
I am trying to parameterize protein and ligand complex along with crystal water.
Can you please direct me how to generate? There are 560 water in crystal structure of protein.
I have already run it through this command:
antechamber -fi pdb -fo mol2 -i WAT_H.pdb -o WAT.mol2-at amber -c bcc -pf y -dr no
Here is the input for sqm:Run semi-empirical minimization
&qmmm
qm_theory='AM1', grms_tol=0.0005,
scfconv=1.d-10, ndiis_attempts=700, qmcharge=0,
/
8 O -14.6250 -1.5500 21.3030
1 H1 -13.6680 -1.5500 21.3030
1 H2 -14.8650 -0.6230 21.3030
8 O -26.6640 -27.0540 16.5150
1 H1 -25.7070 -27.0540 16.5150
1 H2 -26.9040 -26.1270 16.5150
8 O -19.0830 -17.0780 21.6480
1 H1 -18.1260 -17.0780 21.6480
1 H2 -19.3230 -16.1510 21.6480
8 O -7.9350 -6.3420 1.2950....
And the output file (sqm.out) stopped at this:
…….
QMMM: 989 989 H -17.4370 -0.9490 36.9620
QMMM: 990 990 H -18.6340 -0.0220 36.9620
QMMM: 991 991 O -9.7060 10.7040 17.9070
QMMM: 992 992 H -8.7490 10.7040 17.9070
QMMM: 993 993 H -9.9460 11.6310 17.9070
QMMM: 994 994 O -26.1090 6.2790 19.7550
QMMM: 995 995 H -25.1520 6.2790 19.7550
QMMM: 996 996 H -26.3490 7.2060 19.7550
QMMM: 997 997 O -23.4160 9.1110 18.6120
QMMM: 998 998 H -22.4590 9.1110 18.6120
QMMM: 999 999 H -23.6560 10.0380 18.6120--------------------------------------------------------------------------------
RESULTS
-------------------------------------------------------------------------------- iter sqm energy rms gradient
---- ------------------- -----------------------
xmin 10 -20278.8965 kcal/mol 2.8979 kcal/(mol*A)
xmin 20 -20820.3242 kcal/mol 2.7131 kcal/(mol*A)
xmin 30 -21129.5884 kcal/mol 1.3588 kcal/(mol*A)
xmin 40 -21327.1301 kcal/mol 1.8634 kcal/(mol*A)
Its like this from last 24 hours, stopped at this last line (no other log or output file for error). I don't know, is this the right way to parameterize along with all water or should I just take 5 angstrom crystal water around substrate?
Looking forward to see your response.
Thanks,Hira Jabeen
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Received on Wed Mar 25 2020 - 11:00:02 PDT
