From owner-chemistry@ccl.net Sat Nov 17 01:51:00 2007 From: "neeraj Misra neerajmisra]*[hotmail.com" To: CCL Subject: CCL: DFT FOR BEGINNERS Message-Id: <-35622-071117014946-31197-Qn44Ow1BkozJxo+aF3a7ng]~[server.ccl.net> X-Original-From: "neeraj Misra" Date: Sat, 17 Nov 2007 01:49:42 -0500 Sent to CCL by: "neeraj Misra" [neerajmisra . hotmail.com] CAN ANYONE SUGGEST ME SOME GOOD LITERATURE REGARDING THE FUNDAMENTALS OF DENSITY FUNCTIONAL THEORY, ANY LINK, PAPER, ARTICLE WHICH IS ACCESSIBLE. HELP SHALL BE GRATEFULLY ACKNOWLEDGED. From owner-chemistry@ccl.net Sat Nov 17 03:24:01 2007 From: "akef afaneh akef_afnh/a\yahoo.com" To: CCL Subject: CCL: DFT FOR BEGINNERS Message-Id: <-35623-071117032227-782-08zHajW8EAWB20JC7S1kBg-.-server.ccl.net> X-Original-From: akef afaneh Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1630887330-1195287735=:72354" Date: Sat, 17 Nov 2007 00:22:15 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: akef afaneh [akef_afnh/a\yahoo.com] --0-1630887330-1195287735=:72354 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit There are a lot of books and articles, such as: 1. A Chemist’s Guide to Density Functional Theory, Wolfram Koch, Max C. Holthausen, 2001 ( This is an excellent book for the Chemists) 2. Molecular Modelling for Beginners, Alan Hinchliffe, 2003. 3. Molecular Modelling Principles and Applications, Andrew R. Leach, 2001. 4. Density Functional Theory of Atoms and Molecules, Parr and Yang, 1989. 5. Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory, Szabo and Ostlund, 1989. 6. The Fundamental of Density Functional Theory, Helmut Eschrig, 1996. 7. Simons J 1991 An experimental chemist’s guide to ab initio quantum chemistry J. Phys. Chem. 95 1017–29. 8. H ead-Gordon M 1996 Quantum chemistry and molecular processes J. Phys. Chem. 100 13 213–25 9. http://www.yu.edu.jo/rawash/495%20info.html 10. http://www.ccl.net/cgi-bin/ccl/message-new?2007+11+15+002 Good Luck "neeraj Misra neerajmisra]*[hotmail.com" wrote: Sent to CCL by: "neeraj Misra" [neerajmisra . hotmail.com] CAN ANYONE SUGGEST ME SOME GOOD LITERATURE REGARDING THE FUNDAMENTALS OF DENSITY FUNCTIONAL THEORY, ANY LINK, PAPER, ARTICLE WHICH IS ACCESSIBLE. HELP SHALL BE GRATEFULLY ACKNOWLEDGED.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- Never miss a thing. Make Yahoo your homepage. --0-1630887330-1195287735=:72354 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit 
There are a lot of books and articles, such as:
1.      A Chemist’s Guide to Density Functional Theory, Wolfram Koch, Max C. Holthausen, 2001 ( This is an excellent book for the Chemists)
2.      Molecular Modelling for Beginners, Alan Hinchliffe, 2003.
3.      Molecular Modelling Principles and Applications, Andrew R. Leach, 2001.
4.      Density Functional Theory of Atoms and Molecules, Parr and Yang, 1989.
5.      Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory, Szabo and Ostlund, 1989.
6.      The Fundamental of Density Functional Theory,
 Helmut Eschrig, 1996.
7.      Simons J 1991 An experimental chemist’s guide to ab initio quantum chemistry J. Phys. Chem. 95 1017–29.
8.      H ead-Gordon M 1996 Quantum chemistry and molecular processes J. Phys. Chem. 100 13 213–25
9.      http://www.yu.edu.jo/rawash/495%20info.html
10.  http://www.ccl.net/cgi-bin/ccl/message-new?2007+11+15+002
 
 
Good Luck
 


"neeraj Misra neerajmisra]*[hotmail.com" <owner-chemistry#ccl.net> wrote:

Sent to CCL by: "neeraj Misra" [neerajmisra . hotmail.com]
CAN ANYONE SUGGEST ME SOME GOOD LITERATURE REGARDING THE FUNDAMENTALS OF DENSITY FUNCTIONAL THEORY, ANY LINK, PAPER, ARTICLE WHICH IS ACCESSIBLE. HELP SHALL BE GRATEFULLY ACKNOWLEDGED.


http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/chemistry/sub_unsub.shtml
http://www.ccl.net/spammers.txt




Never miss a thing. Make Yahoo your homepage. --0-1630887330-1195287735=:72354-- From owner-chemistry@ccl.net Sat Nov 17 07:58:01 2007 From: "akef afaneh akef_afnh__yahoo.com" To: CCL Subject: CCL:G: Transition State Message-Id: <-35624-071117075659-15358-ju4MYHdnXHJY6q6UkB2TYQ a server.ccl.net> X-Original-From: akef afaneh Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-945015699-1195304205=:79417" Date: Sat, 17 Nov 2007 04:56:45 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: akef afaneh [akef_afnh!=!yahoo.com] --0-945015699-1195304205=:79417 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit In general, TS structures can be predicted in Gaussian 03 from: Scanning the potential energy surface Berny Algorithm Transition State Optimizations Using Synchronous Transit-Guided Quasi- Newton (STQN) Methods and Following the Intrinsic Reaction Coordinate (IRC) 1. Scanning the potential energy surface: this is also called Relaxed Potential Energy Surface Scan. In this method, you fixed one of the structural parameters to a certain value, while all the other parameters are optimized. For example; if we want to study the potential energy surface of ethane compound, by changing the bond length; #P HF/STO-3G OPT=Z-MATRIX NOSYMM 0 1 C C 1 R1 H 1 R2 2 A1 H 1 R2 2 A1 3 T1 H 1 R2 2 A1 3 –T1 H 2 R2 1 A1 3 T2 H 2 R2 1 A1 6 T1 H 2 R2 1 A1 6 –T1 R1=1.2 S 10 +0.05 R2=0.91 A1=109.47 T1=120.0 T2=180.0 The line #9 of the z-matrix describes the initial value of 1.2Ao of C1-C2 bond length, R1, which we specify a scan of 10 steps, in each of which the bond length R1 is varied by +0.05 Ao. As you see, we add nosymm keyword to avoid the problems caused through changes in the point group. No need to use it, if there is no change in the symmetry of the molecule, O.K. Summary of Optimized Potential Surface Scan 1 2 3 4 5 EIGENVALUES -- -78.16801 -78.21443 -78.24867 -78.27314 -78.28974 R1 1.20000 1.25000 1.30000 1.35000 1.40000 R2 1.08892 1.08816 1.08751 1.08701 1.08665 A1 114.46753 113.81850 113.20970 112.62530 112.08172 T1 120.00000 120.00000 120.00000 120.00000 120.00000 T2 180.00000 180.00000 180.00000 180.00000 180.00000 6 7 8 9 10 EIGENVALUES -- -78.30000 -78.30512 -78.30607 -78.30364 -78.29844 R1 1.45000 1.50000 1.55000 1.60000 1.65000 R2 1.08637 1.08617 1.08601 1.08589 1.08582 A1 111.56798 111.08145 110.61991 110.18157 109.77581 T1 120.00000 120.00000 120.00000 120.00000 120.00000 T2 180.00000 180.00000 180.00000 180.00000 180.00000 11 EIGENVALUES -- -78.29099 R1 1.70000 R2 1.08576 A1 109.37959 T1 120.00000 T2 180.00000 2. Berny Algorithm: If the structures of the reactant and product are known, one can construct, guessing, a model of TS as a midpoint between the two, or by using a series of relaxed potential energy scans. Let us take the most popular example in the world; isomerization of HCN to CNH: #P HF/STO-3G OPT=(z-matrix, ts, calcfc, noeigen) 0 1 N C 1 R1 H 2 R2 1 A R1=1.16 R2=1.15 A=90.0 In this method, more than one negative eigenvalue might appear in the Hessian matrix, so, we turn off checking the eigenvalues with noeigen. After each optimization step, the output file contains the current Hessian matrix, its eigenvalues, as well as the corresponding eigenvector 3. STQN: This method, implemented by H. B. Schlegel and coworkers (C. Peng and H. B. Schlegel, Israel J. Chem . 33, 449 (1994)), uses a quadratic Synchronous Transit approach to get closer to the quadratic region of the transition state and then uses a Quasi-Newton or eigenvector-following algorithm to complete the optimization. This method is usually used when there is a difficult to guess the starting point of the TS structure, Berny Algorithm, and the scanning approach does not work. There are two variants available in Gaussian are used with the keywords: Opt=QST2: needs only the structures of the reactant and the product as input. Opt=QST3: needs the structures of reactant, product and the initial TS as input. Let us take a tautomerism formation (keto-enol tautomerism, see: (chemistry.anu.edu.au/student/fourth/CCLAB/TransStates.html) as an example: A procedure to generate the input for a QST2 calculation would be Optimize the structures for the reactants and products. Incorporate the optimised structures for the reactants and products into the QST2 input file Run the QST2 calculation Run a frequency calculation on the calculated transition state structure. #P HF/sto-3g opt=(QST2,Z-Matrix) ethanal 0 1 C C 1 R2 H 1 R3 2 A3 H 2 R4 1 A4 3 T4 H 2 R5 1 A5 3 T5 O 1 R6 2 A6 3 T6 H 6 R7 1 A7 2 T7 R2 1.504222 R3 1.095230 R4 1.086643 R5 1.086643 R6 1.187732 R7 2.549703 A3 115.348 A4 109.814 A5 109.814 A6 124.374 A7 56.398 T4 58.823 T5 -58.823 T6 180.000 T7 0.000 ethanol 0 1 C C 1 R2 H 1 R3 2 A3 H 2 R4 1 A4 3 T4 H 2 R5 1 A5 3 T5 O 1 R6 2 A6 3 T6 H 6 R7 1 A7 2 T7 R2 1.317859 R3 1.073506 R4 1.076957 R5 1.072623 R6 1.347095 R7 0.948399 A3 122.377 A4 122.357 A5 120.146 A6 126.959 A7 110.362 T4 180.001 T5 0.010 T6 179.999 T7 0.057 -- Stationary point found. ---------------------------- ! Optimized Parameters ! ! (Angstroms and Degrees) ! -------------------------- -------------------------- ! Name Definition TS Reactant Product Derivative Info. ! -------------------------------------------------------------------------------- ! R1 R(1,2) 1.4475 1.5042 1.3179 -DE/DX = 0.0001 ! ! R2 R(1,3) 1.0972 1.0952 1.0735 -DE/DX = 0.0 ! ! R3 R(1,6) 1.2929 1.1877 1.3471 -DE/DX = -0.0001 ! ! R4 R(2,4) 1.087 1.0866 1.077 -DE/DX = 0.0001 ! ! R5 R(2,5) 1.0823 1.0866 1.0726 -DE/DX = 0.0 ! ! R6 R(2,7) 1.4746 1.0816 2.4749 -DE/DX = -0.0001 ! ! R7 R(6,7) 1.1635 2.5497 0.9484 -DE/DX = 0.0001 ! ! A1 A(2,1,3) 136.5052 115.348 122.377 -DE/DX = 0.0 ! ! A2 A(2,1,6) 102.5847 124.374 126.959 -DE/DX = 0.0 ! ! A3 A(3,1,6) 120.8409 120.278 110.664 -DE/DX = 0.0 ! ! A4 A(1,2,4) 108.0859 109.814 122.357 -DE/DX = 0.0 ! ! A5 A(1,2,5) 118.868 109.814 120.146 -DE/DX = 0.0 ! ! A6 A(1,2,7) 67.1673 110.2665 49.2433 -DE/DX = 0.0 ! ! A7 A(4,2,5) 110.2993 107.2052 117.497 -DE/DX = 0.0 ! ! A8 A(4,2,7) 92.6029 109.8446 73.1137 -DE/DX = 0.0 ! ! A9 A(5,2,7) 150.9097 109.8446 169.3893 -DE/DX = 0.0001 ! ! A10 A(1,6,7) 82.1256 56.398 110.362 -DE/DX = 0.0 ! ! D1 D(3,1,2,4) 101.4145 58.823 -179.999 -DE/DX = -0.0001 ! ! D2 D(3,1,2,5) -25.2254 -58.823 0.01 -DE/DX = 0.0 ! ! D3 D(3,1,2,7) -173.4997 180.0 179.974 -DE/DX = -0.0001 ! ! D4 D(6,1,2,4) -81.7694 -121.177 0.0 -DE/DX = 0.0 ! ! D5 D(6,1,2,5) 151.5907 121.177 -179.991 -DE/DX = 0.0 ! ! D6 D(6,1,2,7) 3.3164 0.0 -0.027 -DE/DX = 0.0 ! ! D7 D(2,1,6,7) -3.9115 0.0 0.057 -DE/DX = 0.0 ! ! D8 D(3,1,6,7) 173.5366 180.0 -179.9439 -DE/DX = 0.0001 ! -------------------------------------------------------------------------------- Following the Intrinsic Reaction Coordinate (IRC): This method is done after the TS structure is determined. To understand this method, you can refer to the following link: http://www.gaussian.com/g_ur/k_irc.htm. :-) "Shrin Pal spalindia- -gmail.com" wrote: Dear Colleagues, Is it possible to follow a particular bond breaking (TS search corresponding to that bond) in Gaussian 03? In other words, can I specify the bond which I want to break in the TS? Thanking you all, S.P --------------------------------- Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it now. --0-945015699-1195304205=:79417 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
In general, TS structures can be predicted in Gaussian 03 from:
  1. Scanning the potential energy surface
  2. Berny Algorithm
  3. Transition State Optimizations Using Synchronous Transit-Guided Quasi- Newton (STQN) Methods and
  4. Following the Intrinsic Reaction Coordinate (IRC)
 
1. Scanning the potential energy surface: this is also called Relaxed Potential Energy Surface Scan. In this method, you fixed one of the structural parameters to a certain value, while all the other parameters are optimized. For example; if we want to study the potential energy surface of ethane compound, by changing the bond length;
#P HF/STO-3G OPT=Z-MATRIX NOSYMM
 
0 1
C
C 1 R1
H 1 R2 2 A1
H 1 R2 2 A1 3 T1
H 1 R2 2 A1 3 –T1
H 2 R2 1 A1 3 T2
H 2 R2 1 A1 6 T1
H 2 R2 1 A1 6 –T1
 
R1=1.2 S 10 +0.05
R2=0.91
A1=109.47
T1=120.0
T2=180.0
 
The line #9 of the z-matrix describes the initial value of 1.2Ao of C1-C2 bond length, R1, which we specify a scan of 10 steps, in each of which the bond length R1 is varied by +0.05 Ao. As you see, we add nosymm keyword to avoid the problems caused through changes in the point group. No need to use it, if there is no change in the symmetry of the molecule, O.K.
 
Summary of Optimized Potential Surface Scan
                           1         2         3         4         5
     EIGENVALUES --   -78.16801 -78.21443 -78.24867 -78.27314 -78.28974
           R1           1.20000   1.25000   1.30000   1.35000   1.40000
           R2           1.08892   1.08816   1.08751   1.08701   1.08665
           A1         114.46753 113.81850 113.20970 112.62530 112.08172
           T1         120.00000 120.00000 120.00000 120.00000 120.00000
           T2         180.00000 180.00000 180.00000 180.00000 180.00000
                           6         7         8         9        10
     EIGENVALUES --   -78.30000 -78.30512 -78.30607 -78.30364 -78.29844
           R1           1.45000   1.50000   1.55000   1.60000   1.65000
           R2           1.08637   1.08617   1.08601   1.08589   1.08582
           A1         111.56798 111.08145 110.61991 110.18157 109.77581
           T1         120.00000 120.00000 120.00000 120.00000 120.00000
           T2         180.00000 180.00000 180.00000 180.00000 180.00000
                          11
     EIGENVALUES --   -78.29099
           R1           1.70000
           R2           1.08576
           A1         109.37959
           T1         120.00000
           T2         180.00000
 
2. Berny Algorithm: If the structures of the reactant and product are known, one can construct, guessing, a model of TS as a midpoint between the two, or by using a series of relaxed potential energy scans. Let us take the most popular example in the world; isomerization of HCN to CNH:
#P HF/STO-3G OPT=(z-matrix, ts, calcfc, noeigen)
 
0 1
N
C 1 R1
H 2 R2 1 A
 
R1=1.16
R2=1.15
A=90.0
 
In this method, more than one negative eigenvalue might appear in the Hessian matrix, so, we turn off checking the eigenvalues with noeigen. After each optimization step, the output file contains the current Hessian matrix, its eigenvalues, as well as the corresponding eigenvector
 
3. STQN: This method, implemented by H. B. Schlegel and coworkers (C. Peng and H. B. Schlegel, Israel J. Chem . 33, 449 (1994)), uses a quadratic Synchronous Transit approach to get closer to the quadratic region of the transition state and then uses a Quasi-Newton or eigenvector-following algorithm to complete the optimization. This method is usually used when there is a difficult to guess the starting point of the TS structure, Berny Algorithm, and the scanning approach does not work. There are two variants available in Gaussian are used with the keywords:
Opt=QST2: needs only the structures of the reactant and the product as input.
Opt=QST3: needs the structures of reactant, product and the initial TS as input.
Let us take a tautomerism formation (keto-enol tautomerism, see:
(chemistry.anu.edu.au/student/fourth/CCLAB/TransStates.html) as an example: A procedure to generate the input for a QST2 calculation would be
  1. Optimize the structures for the reactants and products.
  2. Incorporate the optimised structures for the reactants and products into the QST2 input file
  3. Run the QST2 calculation
  4. Run a frequency calculation on the calculated transition state structure.
#P HF/sto-3g opt=(QST2,Z-Matrix)
ethanal
 
 0 1
 C
 C   1 R2
 H  1 R3        2 A3
 H  2 R4        1 A4         3 T4
 H  2 R5        1 A5         3 T5
 O  1 R6        2 A6         3 T6
 H  6 R7        1 A7         2 T7
 
R2         1.504222
R3         1.095230 
R4         1.086643 
R5         1.086643 
R6         1.187732 
R7         2.549703
A3        115.348 
A4        109.814 
A5        109.814 
A6        124.374 
A7         56.398
T4         58.823
T5        -58.823
T6        180.000
T7          0.000
 
ethanol   
 
 0 1
 C
 C  1 R2
 H  1 R3        2 A3
 H  2 R4        1 A4         3 T4
 H  2 R5        1 A5         3 T5
 O  1 R6        2 A6         3 T6
 H  6 R7        1 A7         2 T7
 
R2         1.317859
R3         1.073506 
R4         1.076957 
R5         1.072623 
R6         1.347095 
R7         0.948399
A3        122.377
A4        122.357
 
A5        120.146 
A6        126.959 
A7        110.362
T4        180.001
T5          0.010
T6        179.999
T7          0.057
 
-- Stationary point found.
                           ----------------------------
                           !   Optimized Parameters   !
                           ! (Angstroms and Degrees)  !
 --------------------------                            --------------------------
 ! Name  Definition        TS        Reactant  Product Derivative Info.         !
 --------------------------------------------------------------------------------
 ! R1    R(1,2)             1.4475    1.5042    1.3179 -DE/DX =    0.0001       !
 ! R2    R(1,3)             1.0972    1.0952    1.0735 -DE/DX =    0.0          !
 ! R3    R(1,6)            
 1.2929    1.1877    1.3471 -DE/DX =   -0.0001       !
 ! R4    R(2,4)             1.087     1.0866    1.077  -DE/DX =    0.0001       !
 ! R5    R(2,5)             1.0823    1.0866    1.0726 -DE/DX =    0.0          !
 ! R6    R(2,7)             1.4746    1.0816    2.4749 -DE/DX =   -0.0001       !
 ! R7    R(6,7)             1.1635    2.5497    0.9484 -DE/DX =    0.0001       !
 ! A1    A(2,1,3)         136.5052  115.348   122.377  -DE/DX =    0.0          !
 !
 A2    A(2,1,6)         102.5847  124.374   126.959  -DE/DX =    0.0          !
 ! A3    A(3,1,6)         120.8409  120.278   110.664  -DE/DX =    0.0          !
 ! A4    A(1,2,4)         108.0859  109.814   122.357  -DE/DX =    0.0          !
 ! A5    A(1,2,5)         118.868   109.814   120.146  -DE/DX =    0.0          !
 ! A6    A(1,2,7)          67.1673  110.2665   49.2433 -DE/DX =    0.0          !
 ! A7    A(4,2,5)         110.2993  107.2052  117.497  -DE/DX =    0.0          !
 ! A8    A(4,2,7)          92.6029  109.8446   73.1137 -DE/DX =    0.0          !
 ! A9    A(5,2,7)         150.9097  109.8446  169.3893 -DE/DX =    0.0001       !
 ! A10   A(1,6,7)         
 82.1256   56.398   110.362  -DE/DX =    0.0          !
 ! D1    D(3,1,2,4)       101.4145   58.823  -179.999  -DE/DX =   -0.0001       !
 ! D2    D(3,1,2,5)       -25.2254  -58.823     0.01   -DE/DX =    0.0          !
 ! D3    D(3,1,2,7)      -173.4997  180.0     179.974  -DE/DX =   -0.0001       !
 ! D4    D(6,1,2,4)       -81.7694 -121.177     0.0    -DE/DX =    0.0          !
 ! D5    D(6,1,2,5)       151.5907  121.177  -179.991  -DE/DX =    0.0          !
 ! D6    D(6,1,2,7)         3.3164    0.0      -0.027  -DE/DX =    0.0          !
 ! D7    D(2,1,6,7)        -3.9115    0.0       0.057  -DE/DX =    0.0          !
 ! D8    D(3,1,6,7)       173.5366  180.0    -179.9439 -DE/DX =    0.0001       !
 --------------------------------------------------------------------------------
 
  1. Following the Intrinsic Reaction Coordinate (IRC): This method is done after the TS structure is determined. To understand this method, you can refer to the following link: http://www.gaussian.com/g_ur/k_irc.htm. :-)   
 
 
 
 
 


"Shrin Pal spalindia- -gmail.com" <owner-chemistry]![ccl.net> wrote:
Dear Colleagues,

Is it possible to follow a particular bond breaking (TS search corresponding to that bond) in Gaussian 03?
In other words, can I specify the bond which I want to break in the TS?

Thanking you all,

S.P


Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it now. --0-945015699-1195304205=:79417-- From owner-chemistry@ccl.net Sat Nov 17 09:30:00 2007 From: "Yubo Fan yubofan . mail.chem.tamu.edu" To: CCL Subject: CCL:G: Five-coordinated phosphorus Message-Id: <-35625-071117092810-12190-lNCaeN/Gjrxn1q7of8ZvEw:+:server.ccl.net> X-Original-From: "Yubo Fan" Date: Sat, 17 Nov 2007 09:28:06 -0500 Sent to CCL by: "Yubo Fan" [yubofan_-_mail.chem.tamu.edu] Hello, I need to include a five-coordinated phosphorus compound in my simulations. The geometry and esp were calculated by using Gaussian 03. But when I tried to prepare the prepin file, antechamber failed to generate ac files. The error message is: Warning: the assigned bond types may be wrong, please : (1) double check the structure (the connectivity) and/or (2) adjust atom valence penalty parameters in APS.DAT, and/or (3) increase MAXVASTATE in define.h and recompile bondtype.C (4) increase PSCUTOFF in define.h and recompile bondtype.C Be cautious, use a large value of PSCUTOFF (>10) will significantly increase the computer time Error: cannot run "/opt/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in judgebondtype() of antechamber.c properly, exit I tried to edit the APS.DAT but I really don't understand the meaning of the columns in the file. I don't need to add a new atom type to the gaff. I can create a seperate force field file on my own. I only need the prepin file even if the atom type for the five-coordiated phosphorus is the same as that for phosphate. I can change it later. Any advice? Regards, Yubo Fan Chemistry Dept. TAMU From owner-chemistry@ccl.net Sat Nov 17 13:59:01 2007 From: "Roger Kevin Robinson r.robinson{=}imperial.ac.uk" To: CCL Subject: CCL: Lennard Jones Parameter / Critical Temp / Critical Pres Message-Id: <-35626-071116144214-10672-yWOzGPw9yPL7qoCuEGDOdg]~[server.ccl.net> X-Original-From: Roger Kevin Robinson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 16 Nov 2007 18:56:29 +0000 MIME-Version: 1.0 Sent to CCL by: Roger Kevin Robinson [r.robinson a imperial.ac.uk] Hi CCL, Im trying to calculate rate constants for a series of small hydrocarbons. The software requires either I need either the Lennard Jones Parameters, or the Critical Temp/Critical Pressure and the Accentric Values. Does anyone know if there is any way of calculating these values computationally. Or do I need to look them up from experimental data. Presentably a Molecular Mechanics force fields have the Lennards Jones Parameters for the atoms, is it possible to extrapolate to the molecule as a whole ? Any help Appreciated Roger