Dear Amber users and developers,
I have tried to build our own parameters by performing QM calculations on HEME-Fe-HIS system by Guassain 09 (b3lyp/genecp nosymm iop(6/33=2,6/42=6,6/50=1) pop= (mk,readradii) pseudo=read). When I use this output file to produce mol2 file by antechamber, one error happened. The message said: "For atom[7]:Fe1, the best APS is not zero, bonds involved by this atom are frozen". After I run parmchk with that mol2 file, I found that their was no any MASS, BOND, ANGLE and DIHE parameters of Fe and relative atom in frcmod file. However, in my system, I need these parameters to save prmtop files for MD run. (D.A. Giammona's heme paremeter files have not involved these parmerters such as bond parameter for NA-FE and angle parameter for CW - NA – FE, H - NA – FE and NA - FE – NO, etc.) So, what should I do to solve this problem?
remark goes here
MASS
c3 12.010 0.878
cc 12.010 0.360
na 14.010 0.530
cd 12.010 0.360
nd 14.010 0.530
Fe 0.000 0.000 ATTN, need revision ; This value can be found in Giammona's heme paremeters
ce 12.010 0.360
c 12.010 0.616
o 16.000 0.434
cf 12.010 0.360
c2 12.010 0.360
hc 1.008 0.135
hn 1.008 0.161
h4 1.008 0.135
h5 1.008 0.135
ha 1.008 0.135
BOND
c3-cc 337.30 1.499
c3-hc 337.30 1.092
cc-na 438.80 1.371
cc-cd 504.00 1.371
na-hn 406.60 1.011
cd-nd 431.60 1.376
cd-h4 350.10 1.083
cc-nd 494.60 1.335
cc-h5 356.00 1.079
ce-cc 387.90 1.453
ce-cd 511.30 1.367
ce-ha 341.50 1.089
cc-cc 418.30 1.429
cd-cd 418.30 1.429
cd-c3 337.30 1.499
c3-c3 303.10 1.535
c3-c 328.30 1.508
c -o 648.00 1.214
cd-cf 387.90 1.453
cf-c2 560.50 1.339
cf-ha 341.50 1.089
c2-ha 344.30 1.087
cc-h4 350.10 1.083
ANGLE
c3-cc-na 65.500 122.780
c3-cc-cd 64.810 119.450
cc-c3-hc 47.200 110.860
cc-na-cc 68.940 109.900
cc-na-hn 47.020 125.500
cc-cd-nd 72.010 111.750
cc-cd-h4 47.190 129.110
na-cc-cd 72.910 109.420
na-cc-nd 74.780 112.020
na-cc-h5 49.760 122.100
cd-nd-cc 71.080 105.670
nd-cd-h4 50.000 120.030
nd-cc-h5 50.130 125.380
ce-cc-nd 67.800 121.510
ce-cc-cc 62.780 127.200
ce-cd-nd 68.220 124.900
ce-cd-cd 65.880 122.590
nd-cc-cc 71.150 112.560
nd-cd-cd 67.530 121.690
cc-ce-cd 63.280 130.360
cc-ce-ha 47.530 115.450
cc-cc-cd 68.160 114.190
cc-cc-c3 64.660 115.970
cc-cd-cd 68.160 114.190
cc-cd-c3 64.810 119.450
cc-c3-c3 63.580 111.890
cd-c3-hc 47.200 110.860
cd-ce-ha 49.970 115.480
cd-cd-c3 64.660 115.970
c3-c3-c 63.790 110.530
c3-c3-hc 46.370 110.050
c3-c -o 68.030 123.110
c -c3-hc 47.200 109.680
o -c -o 78.170 130.380
cc-cd-cf 63.670 128.410
cd-cf-c2 65.620 123.270
cd-cf-ha 47.530 115.450
cd-cd-cf 62.780 127.200
cf-c2-ha 49.570 121.190
c2-cf-ha 49.560 121.100
cd-c3-c3 63.580 111.890
na-cc-h4 50.220 119.660
cd-cc-h4 47.190 129.110
hc-c3-hc 39.430 108.350
ha-c2-ha 38.020 117.650
DIHE
c3-cc-na-cc 1 1.700 180.000 2.000
c3-cc-na-hn 1 1.700 180.000 2.000
c3-cc-cd-nd 1 4.000 180.000 2.000
c3-cc-cd-h4 1 4.000 180.000 2.000
cc-na-cc-nd 1 1.700 180.000 2.000
cc-na-cc-h5 1 1.700 180.000 2.000
cc-cd-nd-cc 1 4.750 180.000 2.000
na-cc-c3-hc 1 0.000 0.000 3.000
na-cc-cd-nd 1 4.000 180.000 2.000
na-cc-cd-h4 1 4.000 180.000 2.000
na-cc-nd-cd 1 4.750 180.000 2.000
cd-cc-c3-hc 1 0.000 0.000 3.000
cd-cc-na-cc 1 1.700 180.000 2.000
cd-cc-na-hn 1 1.700 180.000 2.000
cd-nd-cc-h5 1 4.750 180.000 2.000
cc-nd-cd-h4 1 4.750 180.000 2.000
nd-cc-na-hn 1 1.700 180.000 2.000
……
…………………………………………………………………………………………
Thank you!
Allen Zou
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Received on Sun Jun 05 2016 - 08:30:03 PDT
