>Hello,
>
>I'm using G09 version B01 and am running into problems when running the fix script. (http://ambermd.org/bugfixesat.html)
>
>I create a gcrt file in antechamber, which is then submitted to G09 to produce a log file, which looks fine as far as I'm concerned.
>
>This is the gcrt file I use:
>
>--Link1--
>%chk=molecule
>#HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt
>
>remark line goes here
>
>1 1
> N 0.0000 0.0000 0.0000
> C -1.5017 -0.2968 -0.2244
> H -1.6076 -0.4784 -1.2889
> H -1.7198 -1.1716 0.3794
> H -2.0280 0.5915 0.1093
> C 0.8395 -1.2191 -0.4501
> H 0.6164 -1.3545 -1.5033
> H 1.8734 -0.9454 -0.2668
> H 0.5041 -2.0477 0.1650
> C 0.2528 0.2742 1.5015
> H -0.3614 1.1339 1.7488
> H -0.0532 -0.6292 2.0189
> H 1.3160 0.4731 1.5871
> C 0.4094 1.2417 -0.8270
> H -0.2125 2.0530 -0.4632
> H 1.4649 1.3922 -0.6249
> H 0.2078 0.9831 -1.8614
>
>Then, I use the fix to create a file: read.com, which I then resubmit to G09. Somehow, the read.log file changes the Mulliken charges from the first gaussian run.
>
>The .com file reads as follows:
>
> %chk=molecule
>#p geom=allcheck chkbas guess=(read,only) density=check
>nosymm prop=(potential,read) pop=minimal
>
> 1.867102 1.659532 0.958262
> 1.524944 1.917918 0.958262
> (...... long list of positions)
>
>And the charges change from:
>
> Mulliken atomic charges:
> 1
> 1 N -0.615407
> 2 C -0.310128
> 3 H 0.238003
> 4 H 0.237990
> 5 H 0.237999
> 6 C -0.310131
> 7 H 0.238005
> 8 H 0.237995
> 9 H 0.237994
> 10 C -0.310136
> 11 H 0.237995
> 12 H 0.237992
> 13 H 0.238011
> 14 C -0.310162
> 15 H 0.238006
> 16 H 0.237986
> 17 H 0.237986
> Sum of Mulliken atomic charges = 1.00000
> Mulliken charges with hydrogens summed into heavy atoms:
> 1
> 1 N -0.615407
> 2 C 0.403864
> 6 C 0.403863
> 10 C 0.403863
> 14 C 0.403817
> Sum of Mulliken charges with hydrogens summed into heavy atoms = 1.00000
>
>To this is the read.log file:
>
> Mulliken atomic charges:
> 1
> 1 N 0.077766
> 2 C 0.916332
> 3 H 0.698103
> 4 H 0.706640
> 5 H 0.665199
> 6 C 0.753884
> 7 H 0.651518
> 8 H 0.240601
> 9 H 0.642690
> 10 C 0.675844
> 11 H 0.578861
> 12 H 0.677318
> 13 H 0.224262
> 14 C 0.624429
> 15 H 0.612642
> 16 H 0.220238
> 17 H 0.622017
> Sum of Mulliken atomic charges = 9.58834
> Mulliken charges with hydrogens summed into heavy atoms:
> 1
> 1 N 0.077766
> 2 C 2.986273
> 6 C 2.288694
> 10 C 2.156284
> 14 C 2.079326
> Sum of Mulliken charges with hydrogens summed into heavy atoms = 9.58834
>
>And, my final mol2 file, created in Antechamber with the command: antechamber -i read.gout -fi gout -nc 1 -c resp -rn hxt -o hxt.mol2 -fo mol2
> reads:
>
>.<TRIPOS>MOLECULE
>hxt
> 17 16 1 0 0
>SMALL
>resp
>
>
>.<TRIPOS>ATOM
> 1 N1 0.0000 0.0000 0.0000 n4 1 hxt 61.717788
> 2 C1 -1.4520 -0.2870 -0.2170 c3 1 hxt 1.411743
> 3 H1 -1.6210 -0.4770 -1.2660 hx 1 hxt -5.530397
> 4 H2 -1.7310 -1.1540 0.3630 hx 1 hxt -5.530397
> 5 H3 -2.0310 0.5670 0.0990 hx 1 hxt -5.530397
> 6 C2 0.8120 -1.1790 -0.4350 c3 1 hxt 1.411743
> 7 H4 0.6310 -1.3640 -1.4830 hx 1 hxt -5.530397
> 8 H5 1.8580 -0.9650 -0.2760 hx 1 hxt -5.530397
> 9 H6 0.5210 -2.0410 0.1460 hx 1 hxt -5.530397
> 10 C3 0.2440 0.2650 1.4520 c3 1 hxt 1.411743
> 11 H7 -0.3440 1.1160 1.7590 hx 1 hxt -5.530397
> 12 H8 -0.0430 -0.6050 2.0230 hx 1 hxt -5.530397
> 13 H9 1.2940 0.4710 1.6010 hx 1 hxt -5.530397
> 14 C4 0.3960 1.2010 -0.8000 c3 1 hxt 1.411743
> 15 H10 -0.1930 2.0470 -0.4810 hx 1 hxt -5.530397
> 16 H11 1.4440 1.4020 -0.6380 hx 1 hxt -5.530397
> 17 H12 0.2170 1.0020 -1.8460 hx 1 hxt -5.530397
>.<TRIPOS>BOND
> 1 1 2 1
> 2 1 6 1
> 3 1 10 1
> 4 1 14 1
> 5 2 3 1
> 6 2 4 1
> 7 2 5 1
> 8 6 7 1
> 9 6 8 1
> 10 6 9 1
> 11 10 11 1
> 12 10 12 1
> 13 10 13 1
> 14 14 15 1
> 15 14 16 1
> 16 14 17 1
>.<TRIPOS>SUBSTRUCTURE
> 1 hxt 1 TEMP 0 **** **** 0 ROOT
>
>What am I doing incorrectly??
>
>Thanks,
>Lisa Felberg
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Received on Fri Feb 17 2012 - 08:30:02 PST
