Dear Thomas,
See
http://q4md-forcefieldtools.org/REDDB/projects/F-90/
or
http://q4md-forcefieldtools.org/REDDB/projects/F-91/
with two types of phosphate groups...
-OPO3(2-)
-OPO2(-)OH
Fan, this clearly shows that all the combinations of phosphate groups
and their oligomerization are needed for these cofactors ;-)
regards, Francois
> I hope that this was not answered before but I did not find anything in
> the AMBER mailing list achive.
>
> I try to generate parameters for a modifide UTP with antechamber. When
> all phosphate groups are completely deprotonated, I see a proton
> transfer from the sugar ring to the terminal phospate group in sqm.out.
> Even if this might be a reasonable reaction in vacuo, the obtained
> partial charges are completely useless, since they correspond to another
> "tautomer". Is it possible to just use the non-optimized structure for
> the calculation of the partial charges or is there a better way to do it?
>
> I also tried to get parameters for UTP with one proton attached to the
> terminal phosphate group. Here sqm give a reasonable structure and the
> parameterization ends without errors. When I, however, use these
> parameters in an energy minimization, the proton gets very close to one
> phosphorus and the electrostatic energy approaches -inf. In contrast,
> the VDW energy does not change at all and, thus, it seem that VDW
> parameters are missing in the input files. Below are the corresponding
> mol2 and frcmod files from antechamber and the leap.in file.
>
> Thank you very much.
> Thomas
>
> .<TRIPOS>MOLECULE
> LIG#
> 42 43 1 0 0
> SMALL
> bcc
>
>
> .<TRIPOS>ATOM
> 1 C01 -9.0320 -31.5650 11.1630 cc 1 LIG# -0.382200
> 2 C02 -9.3870 -32.5860 10.1920 cd 1 LIG# 0.100600
> 3 C07 -9.7670 -31.4330 12.4210 c 1 LIG# 0.721700
> 4 N03 -10.4740 -33.4250 10.5130 n 1 LIG# -0.345000
> 5 N06 -10.8580 -32.3250 12.6790 n 1 LIG# -0.601500
> 6 O08 -9.4550 -30.5970 13.2810 o 1 LIG# -0.700500
> 7 C04 -11.2760 -33.3380 11.7490 c 1 LIG# 0.803500
> 8 C09 -10.8080 -34.3260 9.4770 c3 1 LIG# 0.285500
> 9 H1 -11.3660 -32.2360 13.5710 hn 1 LIG# 0.319500
> 10 O05 -12.2380 -34.0410 12.0340 o 1 LIG# -0.690500
> 11 C10 -9.8930 -35.4280 9.2560 c3 1 LIG# 0.129100
> 12 O13 -12.0200 -34.9580 9.6660 os 1 LIG# -0.452600
> 13 C11 -10.6430 -36.2020 8.3050 c3 1 LIG# 0.104100
> 14 O29 -8.7670 -34.8550 8.7030 oh 1 LIG# -0.650800
> 15 C12 -12.0540 -35.9180 8.6480 c3 1 LIG# 0.109100
> 16 O28 -10.3940 -35.7200 7.0490 oh 1 LIG# -0.633800
> 17 C14 -12.7740 -37.1540 9.0670 c3 1 LIG# 0.180400
> 18 O15 -12.6110 -37.6130 10.3620 os 1 LIG# -0.601200
> 19 P16 -11.9680 -39.0010 10.7100 p5 1 LIG# 1.465700
> 20 N19 -10.2980 -38.9350 10.6110 n3 1 LIG# -0.989400
> 21 O18 -12.5840 -40.0470 9.8190 o 1 LIG# -0.870500
> 22 O17 -12.2420 -39.3960 12.1250 o 1 LIG# -0.870500
> 23 P20 -9.5640 -40.1360 9.7170 p5 1 LIG# 1.627700
> 24 H2 -9.7550 -38.1940 11.0760 hn 1 LIG# 0.399800
> 25 O21 -10.0020 -39.8980 8.3190 o 1 LIG# -0.921500
> 26 O22 -8.0580 -39.9070 9.7630 o 1 LIG# -0.921500
> 27 O23 -9.9440 -41.5600 10.1620 os 1 LIG# -0.843800
> 28 P24 -8.8850 -42.6320 10.4370 p5 1 LIG# 1.593800
> 29 O25 -9.0130 -43.7270 9.4650 o 1 LIG# -0.895000
> 30 O26 -7.5340 -42.0160 10.4930 o 1 LIG# -0.895000
> 31 O27 -9.1940 -43.2590 11.7180 oh 1 LIG# -0.813400
> 32 H3 -10.0700 -43.6460 11.6480 ho 1 LIG# 0.425000
> 33 H4 -10.8620 -33.7530 8.5390 h2 1 LIG# 0.099700
> 34 H5 -9.6870 -35.9870 10.1810 h1 1 LIG# 0.114700
> 35 H6 -10.4250 -37.2760 8.3980 h1 1 LIG# 0.127700
> 36 H7 -12.5560 -35.5040 7.7610 h1 1 LIG# 0.052700
> 37 H8 -12.4570 -37.9880 8.4230 h1 1 LIG# 0.034200
> 38 H9 -13.8560 -36.9930 8.9520 h1 1 LIG# 0.034200
> 39 H10 -8.2100 -30.8910 10.9520 ha 1 LIG# 0.180000
> 40 H11 -8.8410 -32.6980 9.2620 h4 1 LIG# 0.265000
> 41 H12 -8.9830 -33.9350 8.6050 ho 1 LIG# 0.488000
> 42 H13 -11.1650 -35.2120 6.8240 ho 1 LIG# 0.419000
> .<TRIPOS>BOND
> 1 1 2 2
> 2 1 3 1
> 3 1 39 1
> 4 2 4 1
> 5 2 40 1
> 6 3 5 1
> 7 3 6 2
> 8 4 7 1
> 9 4 8 1
> 10 5 7 1
> 11 5 9 1
> 12 7 10 2
> 13 8 11 1
> 14 8 12 1
> 15 8 33 1
> 16 11 13 1
> 17 11 14 1
> 18 11 34 1
> 19 12 15 1
> 20 13 15 1
> 21 13 16 1
> 22 13 35 1
> 23 14 41 1
> 24 15 17 1
> 25 15 36 1
> 26 16 42 1
> 27 17 18 1
> 28 17 37 1
> 29 17 38 1
> 30 19 18 1
> 31 19 20 1
> 32 19 21 1
> 33 19 22 1
> 34 23 20 1
> 35 20 24 1
> 36 23 25 1
> 37 23 26 1
> 38 23 27 1
> 39 28 27 1
> 40 28 29 1
> 41 28 30 1
> 42 28 31 1
> 43 31 32 1
> .<TRIPOS>SUBSTRUCTURE
> 1 LIG# 1 TEMP 0 **** **** 0 ROOT
>
>
> remark goes here
> MASS
>
> BOND
>
> ANGLE
>
> DIHE
>
> IMPROPER
> c -cd-cc-ha 1.1 180.0 2.0 Using
> default value
> cc-h4-cd-n 1.1 180.0 2.0 Using
> default value
> cc-n -c -o 10.5 180.0 2.0 General
> improper torsional angle (2 general atom types)
> c -c3-n -cd 1.1 180.0 2.0 Using
> default value
> c -c -n -hn 1.1 180.0 2.0 General
> improper torsional angle (2 general atom types)
> n -n -c -o 10.5 180.0 2.0 General
> improper torsional angle (2 general atom types)
>
> NONBON
>
> source leaprc.ff12SB
> source leaprc.gaff
> loadAmberParams MURU_CM04_ligand1_LIG1_0_bindmatch_ante.frcmod
> loadAmberPrep /home-link/cpaex01/INPHARMA-workflow/metals.prp
> loadAmberParams /home-link/cpaex01/INPHARMA-workflow/metals.dat
> loadAmberParams frcmod.tip4pew
> loadAmberParams frcmod.ionsjc_tip4pew
> LIG = loadmol2 MURU_CM04_ligand1_LIG1_0_bindmatch_ante.mol2
> XXX = loadPdb MURU_CM04_complex_bindmatch_amber.pdb
> saveAmberParm XXX MURU_CM04_complex.top MURU_CM04_complex.xyz
> quit
>
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Received on Sat Mar 29 2014 - 00:30:02 PDT
