Dear Lisa,
You could try R.E.D. Server or R.E.D.-III.5
A similar example for chemical equivalencing is at
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#8 with
Cobalt(III)_hexammine
- I started by creating a PDB file for tetramethylammonium:
http://en.wikipedia.org/wiki/Tetramethylammonium_hydroxide
HETATM 1 N1 MEA 1 0.000 0.000 0.000 1.00 0.00 N
HETATM 2 C2 MEA 1 -1.167 0.707 0.612 1.00 0.00 C
HETATM 3 H21 MEA 1 -2.077 0.205 0.318 1.00 0.00 H
HETATM 4 H22 MEA 1 -1.067 0.687 1.687 1.00 0.00 H
HETATM 5 H23 MEA 1 -1.182 1.729 0.264 1.00 0.00 H
HETATM 6 C3 MEA 1 0.030 -1.418 0.476 1.00 0.00 C
HETATM 7 H31 MEA 1 -0.886 -1.907 0.183 1.00 0.00 H
HETATM 8 H32 MEA 1 0.875 -1.921 0.031 1.00 0.00 H
HETATM 9 H33 MEA 1 0.123 -1.426 1.552 1.00 0.00 H
HETATM 10 C4 MEA 1 1.266 0.688 0.401 1.00 0.00 C
HETATM 11 H41 MEA 1 1.237 1.710 0.054 1.00 0.00 H
HETATM 12 H42 MEA 1 1.352 0.668 1.477 1.00 0.00 H
HETATM 13 H43 MEA 1 2.103 0.172 -0.044 1.00 0.00 H
HETATM 14 C5 MEA 1 -0.129 0.023 -1.490 1.00 0.00 C
HETATM 15 H51 MEA 1 -0.150 1.048 -1.826 1.00 0.00 H
HETATM 16 H52 MEA 1 0.716 -0.489 -1.924 1.00 0.00 H
HETATM 17 H53 MEA 1 -1.045 -0.475 -1.772 1.00 0.00 H
- I executed Ante_R.E.D. 2.0 to generate a P2N file:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFFXRsOOzFADFbjynCZWCXZd9la1MADFL9eg1/P6459.html
See the java applet for the P2N file:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFFXRsOOzFADFbjynCZWCXZd9la1MADFL9eg1/P6459/javaappletp2n-1.html
& the corresponding P2N file
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFFXRsOOzFADFbjynCZWCXZd9la1MADFL9eg1/P6459/Mol_antered1-out.p2n
- I set the total charge tetramethylammonium to 1 in this P2N file:
REMARK TITLE Tetramethylammonium
REMARK CHARGE-VALUE 1
REMARK MULTIPLICITY-VALUE 1
- Then, I executed R.E.D. IV using the P2N file to generate a mol2 file:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFzMA7ZFnKADFWFz4Sd8WUIGFogH037YGdADF/P6461.html
with the corresponding java applet:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFzMA7ZFnKADFWFz4Sd8WUIGFogH037YGdADF/P6461/javaappletmol2-1.html
& the corresponding mol2 file
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFzMA7ZFnKADFWFz4Sd8WUIGFogH037YGdADF/P6461/Data-R.E.D.Server/Mol_m1-o1.mol2
.<TRIPOS>ATOM
1 N1 -0.000000 0.000000 -0.000000 N 1 MEA 0.1175
2 C2 0.369652 1.343699 -0.543603 C 1 MEA -0.2163
3 H21 0.291678 1.321553 -1.619960 H 1 MEA 0.1456
4 H22 -0.305179 2.083921 -0.141370 H 1 MEA 0.1456
5 H23 1.383399 1.574147 -0.253207 H 1 MEA 0.1456
6 C3 -1.404133 -0.329417 -0.396955 C 1 MEA -0.2163
7 H31 -1.471689 -0.341746 -1.474174 H 1 MEA 0.1456
8 H32 -1.663340 -1.299673 -0.001313 H 1 MEA 0.1456
9 H33 -2.068549 0.420632 0.004409 H 1 MEA 0.1456
etc...
- Atom types to be added are basic: N3, CT and HP
.<TRIPOS>ATOM
1 N1 -0.000000 0.000000 -0.000000 N3 1 MEA 0.1175
2 C2 0.369652 1.343699 -0.543603 CT 1 MEA -0.2163
3 H21 0.291678 1.321553 -1.619960 HP 1 MEA 0.1456
4 H22 -0.305179 2.083921 -0.141370 HP 1 MEA 0.1456
5 H23 1.383399 1.574147 -0.253207 HP 1 MEA 0.1456
etc...
- See
http://q4md-forcefieldtools.org/REDS/faq.php#21
to exchange data between users using R.E.D. Server
- You will found rounding-off errors for the total charge of your
molecule in the mol2 file format:
Loading Mol2 file: ./Data-R.E.D.Server/Mol_m1-o1.mol2
> charge x1
Total unperturbed charge: 0.999500
R.E.D.-III.5 should now automatically correct (if requested by the
user) mol2 files with rounding off errors in agreement with chemical
equivalencing and any type of constraints used during the charge
fitting step. This approach will be implemented in R.E.D. Server next
week.
For tetramethylammonium rounding-off errors correction is quite
tricky; R.E.D.-III.5 can only correct the error at 1.10-5 e and
neither at 1.10-4 (default) not at 1.10-6...
1 N1 0.117430 0.11743 0.11744 !
2 CT2 -0.216314 -0.21631 -0.21631
3 H2 0.145652 0.14565 0.14565
4 H2 0.145652 0.14565 0.14565
5 H2 0.145652 0.14565 0.14565
6 CT2 -0.216314 -0.21631 -0.21631
7 H2 0.145652 0.14565 0.14565
8 H2 0.145652 0.14565 0.14565
9 H2 0.145652 0.14565 0.14565
10 CT2 -0.216314 -0.21631 -0.21631
11 H2 0.145652 0.14565 0.14565
12 H2 0.145652 0.14565 0.14565
13 H2 0.145652 0.14565 0.14565
14 CT2 -0.216314 -0.21631 -0.21631
15 H2 0.145652 0.14565 0.14565
16 H2 0.145652 0.14565 0.14565
17 H2 0.145652 0.14565 0.14565
Loading Mol2 file: ./Data-RED/Mol_m1-o1.mol2
> charge x1
Total unperturbed charge: 1.000000
I hope this helps...
regards, Francois
>> 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 Sat Feb 18 2012 - 00:00:01 PST
