Hi Maria,
Unfortunately Ruthenium is WAYYYY beyond anything antechamber was ever
designed to do. It is designed for organic ligands. The Gaff force field was
also not designed for such situations so you are going to have to
parameterize the ruthenium yourself along with most likely generating the
charge fitting manually using RESP (or R.E.D.) and then build the frcmod and
lib/mol2 files yourself in Leap.
You might also want to see if anyone else has successfully simulated
ruthenium compounds using classical force fields. I'd be very surprised if
one can get an accurate description using classical MD.
This tutorial might be helpful in building things manually. Don't under
estimate the parameterization task here though.
http://ambermd.org/tutorials/advanced/tutorial1_adv/
All the best
Ross
> -----Original Message-----
> From: Maria Minakova [mailto:mariabiophysics.gmail.com]
> Sent: Thursday, June 28, 2012 2:25 PM
> To: amber.ambermd.org
> Subject: [AMBER] Prepgen omits information about half of the atoms
>
> Hi,
> I'm working on parametrization of Ruthenium-based chromophore for
> further all-atom MD.
> I tried to make prep files by two ways, both failed:
>
> 1) I use g09 output file (see more below) to run antechamber:
> antechamber -i chrom1_12.log -fi gout -o chrom1_12.prepin -fo prepi -c
> resp -at amber -s 2 -gv 1 -ge chrom1_12_respfile.gesp (fail at
> espgen stage)
>
> The error message is:
> espgen cannot deal with Gaussian 09 log file, please generate Gaussian
> 09 ESP file using iop(6/50=1) and rerun espgen
> Error: cannot run "/Users/MariaM/amber12/bin/espgen -o ANTECHAMBER.ESP
> -i chrom1_12.log" in resp() of charge.c properly, exit
>
> ANTECHAMBER.ESP file is empty
>
> 2) after doing step one I run:
> 2.1) respgen -i ANTECHAMBER_AC.AC -o chrom1_12.respin1 -f resp1
> (success)
> 2.2) respgen -i ANTECHAMBER_AC.AC -o chrom1_12.respin2 -f resp2
> (success)
> 2.3) resp -O -i chrom1_12.respin1 -o chrom1_12.respout1 -e
> ANTECHAMBER.ESP -t qout_stage1 (success)
> 2.4) resp -O -i chrom1_12.respin2 -o chrom1_12.respout2 -e
> ANTECHAMBER.ESP -q qout_stage1 -t qout_stage2 (success)
> 2.5) antechamber -i ANTECHAMBER_AC.AC -fi ac -o chrom1_12_resp.ac -fo
> ac -c rc -cf qout_stage2 (success, except for warning)
>
> For atom[110]:Ru1, the best APS is not zero, bonds involved by this
> atom are frozen
>
> 2.6) prepgen -i chrom1_12_resp.ac -o chrom1_12.prepin -f int -rn BZ1
>
> the file chrom1_12.prepin is created, but information about atom# > 58
> is lost:
>
> 0 0 2
>
> This is a remark line
> molecule.res
> BZ1 INT 0
> CORRECT OMIT DU BEG
> 0.0000
> 1 DUMM DU M 0 -1 -2 0.000 .0 .0
> .00000
> 2 DUMM DU M 1 0 -1 1.449 .0 .0
> .00000
> 3 DUMM DU M 2 1 0 1.522 111.1 .0
> .00000
> 4 O2 o M 3 2 1 1.540 111.208 -180.000 -
> 0.486813
> 5 C20 c M 4 3 2 1.242 30.171 -64.174
> 0.434978
> 6 H6 h4 E 5 4 3 1.100 122.239 -24.438
> 0.056907
> 7 C17 c3 M 5 4 3 1.548 121.602 157.515 -
> 0.027186
> 8 C19 c3 B 7 5 4 1.545 112.191 41.627 -
> 0.083785
> 9 H5 hc E 8 7 5 1.095 109.037 -28.431
> 0.096385
> 10 H7 hc E 8 7 5 1.094 112.405 92.948
> 0.096385
> 11 H3 h1 E 7 5 4 1.098 107.838 166.763
> 0.060995
> 12 N7 n M 7 5 4 1.493 111.519 -73.624 -
> 0.095454
> 13 C41 c B 12 7 5 1.379 118.989 -51.578
> 0.534850
> 14 O15 o E 13 12 7 1.262 119.178 1.195 -
> 0.570831
> 15 C42 c3 3 13 12 7 1.518 117.858 -178.684 -
> 0.197609
> 16 H41 hc E 15 13 12 1.091 108.368 -174.594
> 0.075016
> 17 H42 hc E 15 13 12 1.098 111.559 -54.574
> 0.075016
> 18 H43 hc E 15 13 12 1.098 111.088 66.131
> 0.075016
> 19 C16 c3 M 12 7 5 1.473 113.422 124.445 -
> 0.135613
> 20 H1 h1 E 19 12 7 1.098 111.922 -98.958
> 0.108381
> 21 H2 h1 E 19 12 7 1.095 111.608 138.514
> 0.108381
> 22 C18 c3 M 19 12 7 1.550 102.210 18.424 -
> 0.173188
> 23 H4 h1 E 22 19 12 1.096 110.023 85.429
> 0.136263
> 24 N1 na M 22 19 12 1.476 112.739 -155.655
> 0.518912
> 25 C1 cc S 24 22 19 1.376 129.296 -126.583 -
> 0.448171
> 26 H8 h4 E 25 24 22 1.077 122.913 2.266
> 0.238542
> 27 N2 nc M 24 22 19 1.385 119.748 56.041 -
> 0.419388
> 28 N3 nd M 27 24 22 1.337 106.237 177.922 -
> 0.075864
> 29 C2 cd M 28 27 24 1.389 109.811 -0.077
> 0.257406
> 30 C3 c3 M 29 28 27 1.509 119.083 -179.773 -
> 0.054636
> 31 H9 h1 E 30 29 28 1.098 111.739 -116.181
> 0.107542
> 32 H10 h1 E 30 29 28 1.097 111.835 124.263
> 0.107542
> 33 N4 n M 30 29 28 1.472 106.718 4.079 -
> 0.165437
> 34 H11 hn E 33 30 29 1.020 113.483 -3.047 -
> 0.008955
> 35 C4 c M 33 30 29 1.354 122.615 177.176
> 0.459953
> 36 O1 o E 35 33 30 1.263 124.046 1.137 -
> 0.539587
> 37 C5 ca M 35 33 30 1.519 116.862 -178.562
> 0.040550
> 38 C7 ca B 37 35 33 1.411 125.530 3.043 -
> 0.102250
> 39 C8 ca B 38 37 35 1.401 119.106 178.868 -
> 0.109223
> 40 N5 nb E 39 38 37 1.361 122.679 0.271
> 0.075804
> 41 H14 h4 E 39 38 37 1.082 120.563 -179.666
> 0.140736
> 42 H13 ha E 38 37 35 1.085 122.668 -0.476
> 0.184645
> 43 C6 ca M 37 35 33 1.406 116.412 -177.811 -
> 0.064493
> 44 H12 ha E 43 37 35 1.084 116.865 0.239
> 0.139061
> 45 C9 cp M 43 37 35 1.402 120.557 -179.203
> 0.033360
> 46 C10 cp M 45 43 37 1.478 123.834 179.859
> 0.021187
> 47 N6 nb M 46 45 43 1.377 115.229 -177.718
> 0.102653
> 48 C12 ca M 47 46 45 1.362 118.563 -179.831 -
> 0.138256
> 49 H16 h4 E 48 47 46 1.083 116.634 -179.876
> 0.151130
> 50 C13 ca M 48 47 46 1.398 122.528 -0.237 -
> 0.131907
> 51 H17 ha E 50 48 47 1.086 119.294 -179.750
> 0.171058
> 52 C14 ca M 50 48 47 1.415 120.085 0.301
> 0.164784
> 53 C15 c3 3 52 50 48 1.510 121.507 178.823 -
> 0.330501
> 54 H18 hc E 53 52 50 1.095 111.465 36.533
> 0.132278
> 55 H19 hc E 53 52 50 1.095 111.863 157.969
> 0.132278
> 56 H20 hc E 53 52 50 1.098 110.414 -82.439
> 0.132278
> 57 C11 ca M 52 50 48 1.411 116.877 -0.281 -
> 0.155728
> 58 H15 ha E 57 52 50 1.084 119.277 -179.909
> 0.173412
> 59 X 1 0 1 14.095 nan 0.000
> 0.000000
> 60 X 1 0 1 14.095 nan 0.000
> 0.000000
> 61 X 1 0 1 14.095 nan 0.000
> 0.000000
> 62 X 1 0 1 14.095 nan 0.000
> 0.000000
> 63 X 1 0 1 14.095 nan 0.000
> 0.000000
> 64 X 1 0 1 14.095 nan 0.000
> 0.000000
> 65 X 1 0 1 14.095 nan 0.000
> 0.000000
> 66 X 1 0 1 14.095 nan 0.000
> 0.000000
> 67 X 1 0 1 14.095 nan 0.000
> 0.000000
> 68 X 1 0 1 14.095 nan 0.000
> 0.000000
> 69 X 1 0 1 14.095 nan 0.000
> 0.000000
> 70 X 1 0 1 14.095 nan 0.000
> 0.000000
> 71 X 1 0 1 14.095 nan 0.000
> 0.000000
> 72 X 1 0 1 14.095 nan 0.000
> 0.000000
> 73 X 1 0 1 14.095 nan 0.000
> 0.000000
> 74 X 1 0 1 14.095 nan 0.000
> 0.000000
> 75 X 1 0 1 14.095 nan 0.000
> 0.000000
> 76 X 1 0 1 14.095 nan 0.000
> 0.000000
> 77 X 1 0 1 14.095 nan 0.000
> 0.000000
> 78 X 1 0 1 14.095 nan 0.000
> 0.000000
> 79 X 1 0 1 14.095 nan 0.000
> 0.000000
> 80 X 1 0 1 14.095 nan 0.000
> 0.000000
> 81 X 1 0 1 14.095 nan 0.000
> 0.000000
> 82 X 1 0 1 14.095 nan 0.000
> 0.000000
> 83 X 1 0 1 14.095 nan 0.000
> 0.000000
> 84 X 1 0 1 14.095 nan 0.000
> 0.000000
> 85 X 1 0 1 14.095 nan 0.000
> 0.000000
> 86 X 1 0 1 14.095 nan 0.000
> 0.000000
> 87 X 1 0 1 14.095 nan 0.000
> 0.000000
> 88 X 1 0 1 14.095 nan 0.000
> 0.000000
> 89 X 1 0 1 14.095 nan 0.000
> 0.000000
> 90 X 1 0 1 14.095 nan 0.000
> 0.000000
> 91 X 1 0 1 14.095 nan 0.000
> 0.000000
> 92 X 1 0 1 14.095 nan 0.000
> 0.000000
> 93 X 1 0 1 14.095 nan 0.000
> 0.000000
> 94 X 1 0 1 14.095 nan 0.000
> 0.000000
> 95 X 1 0 1 14.095 nan 0.000
> 0.000000
> 96 X 1 0 1 14.095 nan 0.000
> 0.000000
> 97 X 1 0 1 14.095 nan 0.000
> 0.000000
> 98 X 1 0 1 14.095 nan 0.000
> 0.000000
> 99 X 1 0 1 14.095 nan 0.000
> 0.000000
> 100 X 1 0 1 14.095 nan 0.000
> 0.000000
> 101 X 1 0 1 14.095 nan 0.000
> 0.000000
> 102 X 1 0 1 14.095 nan 0.000
> 0.000000
> 103 X 1 0 1 14.095 nan 0.000
> 0.000000
> 104 X 1 0 1 14.095 nan 0.000
> 0.000000
> 105 X 1 0 1 14.095 nan 0.000
> 0.000000
> 106 X 1 0 1 14.095 nan 0.000
> 0.000000
> 107 X 1 0 1 14.095 nan 0.000
> 0.000000
> 108 X 1 0 1 14.095 nan 0.000
> 0.000000
> 109 X 1 0 1 14.095 nan 0.000
> 0.000000
> 110 X 1 0 1 14.095 nan 0.000
> 0.000000
> 111 X 1 0 1 14.095 nan 0.000
> 0.000000
> 112 X 1 0 1 14.095 nan 0.000
> 0.000000
> 113 X 1 0 1 14.095 nan 0.000
> 0.000000
> 114 X 1 0 1 14.095 nan 0.000
> 0.000000
> 115 X 1 0 1 14.095 nan 0.000
> 0.000000
> 116 X 1 0 1 14.095 nan 0.000
> 0.000000
> 117 X 1 0 1 14.095 nan 0.000
> 0.000000
> 118 X 1 0 1 14.095 nan 0.000
> 0.000000
> 119 X 1 0 1 14.095 nan 0.000
> 0.000000
>
>
> LOOP
> C18 C19
> C2 C1
> C9 N5
> C11 C10
>
> IMPROPER
> C17 H6 C20 O2
> C41 C16 N7 C17
> C42 N7 C41 O15
> C18 C1 N1 N2
> C2 H8 C1 N1
> C3 C1 C2 N3
> C3 C4 N4 H11
> C5 N4 C4 O1
> C4 C7 C5 C6
> C5 C8 C7 H13
> C7 H14 C8 N5
> C5 C9 C6 H12
> C6 C10 C9 N5
> C11 C9 C10 N6
> C13 H16 C12 N6
> C12 C14 C13 H17
> C15 C13 C14 C11
> C14 C10 C11 H15
>
> DONE
> STOP
>
> Additional info:
> The chromophore consists of 116 atoms. I ran DFT to optimize structure
> and get esp charges on Gaussian 09 with the input line:
>
> # opt b3lyp/lanl2dz geom=connectivity pop=(mk,readradii) iop(6/50=1)
>
> ... and last two lines from *.com:
>
> 44 2.0
>
> 44 2.0
>
> Can anything be done to make prepgen process large molecules like this?
>
>
> With best regards, Maria Minakova.
>
>
>
>
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Received on Thu Jun 28 2012 - 15:00:05 PDT
