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From: Marcus M. <ma...@sa...> - 2005-07-28 16:39:24
|
On Jul 27, 2005, at 11:23 PM, Shanmuga Priya Ashokan wrote: > parameters not found for improper > atoms 1 2 6 7 > names: > N_3 > C_3 > H_ > H_ > > No idea why this error is arising?? This error occurs when you setup the input file for a molecule and try to put an improper torsion across atoms for which no parameters exist in the related force field file. Judging from those atom names it looks like you are using the UFF force field. The inversion (aka improper torsion) section of the original UFF paper is quite confusing to me, but I believe it states the sp3 nitrogen inversion term has a zero force constant. Therefore, I didn't bother implementing it into the forcefield as you are just computing extra terms for no effect. I would suggest just leaving out the N_3 improper torsion terms. Marcus ------------------------------------------------------------------- Marcus G. Martin Senior Member of Technical Staff Multiscale Computational Materials Methods Sandia National Laboratories PO Box 5800 MS 1110 Albuquerque NM 87185-1110 v. 505 284-6355 f. 505 845-7442 http://www.cs.sandia.gov/marcusmartin/ http://towhee.sourceforge.net |
|
From: Shanmuga P. A. <pri...@gm...> - 2005-07-28 07:40:16
|
Dear all, I am M.Tech student doing my final year research work on "Minimization of small molecules" using Towhee. In this aspect I am getting the following error when I run minimization. parameters not found for improper atoms 1 2 6 7 names: N_3 C_3 H_ H_ No idea why this error is arising?? Pls help me in this issue. Thankx. A.Shanmuga Priya. Research Student. Sathyabama Institute of Science & technology. |
|
From: Shanmuga P. A. <pri...@gm...> - 2005-07-28 05:23:39
|
Dear all, I am M.Tech student doing my final year research work on "Minimization of small molecules" using Towhee. In this aspect I am getting the following error when I run minimization. parameters not found for improper atoms 1 2 6 7 names: N_3 C_3 H_ H_ No idea why this error is arising?? Pls help me in this issue. Thankx. A.Shanmuga Priya. Research Student. Sathyabama Institute of Science & technology. |
|
From: Marcus M. <ma...@sa...> - 2005-07-25 16:18:27
|
On Jul 24, 2005, at 8:34 PM, li jianguo wrote: > I am=A0a new=A0user=A0of Towhee.=A0I have compiled towhee under Linux = and get=20 > the binary file. I want to try=A0the examples in Example directory, = but=20 > I don't know how to run those examples. I tried several command, like=20= > "towhee <towhee_input> towhee_output" or "towhee <towhee_input", but=20= > they don't work, with the error message: segmentation fault. Could=20 > anybody kindly tell me=A0 the command or=A0provide me the scritpt to = run=20 > the software? You do not need to pipe any files into Towhee to make it run. /towheebase/Source/towhee > towhee_output will generally do the trick where /towheebase is replaced with the=20 directory path for the towhee distribution on your machine. If you are getting a segmentation fault the most likely culprit is not=20= enough memory on your computer. To reduce the memory you need to adjust the variables in preproc.h This file is described=20 in the manual at http://towhee.sourceforge.net/code/code_manual.html#preproc Marcus ------------------------------------------------------------------- Marcus G. Martin Senior Member of Technical Staff Multiscale Computational Materials Methods Sandia National Laboratories PO Box 5800 MS 1110 Albuquerque NM 87185-1110 v. 505 284-6355 f. 505 845-7442 http://www.cs.sandia.gov/marcusmartin/ http://towhee.sourceforge.net ------------------------------------------------------------------- Marcus G. Martin Senior Member of Technical Staff Multiscale Computational Materials Methods Sandia National Laboratories PO Box 5800 MS 1110 Albuquerque NM 87185-1110 v. 505 284-6355 f. 505 845-7442 http://www.cs.sandia.gov/marcusmartin/ http://towhee.sourceforge.net= |
|
From: li j. <lj...@ya...> - 2005-07-25 02:35:58
|
Dear all, I am a new user of Towhee. I have compiled towhee under Linux and get the binary file. I want to try the examples in Example directory, but I don't know how to run those examples. I tried several command, like "towhee <towhee_input> towhee_output" or "towhee <towhee_input", but they don't work, with the error message: segementation fault. Could anybody kindly tell me the command or provide me the scritpt to run the software? Thanks in advance, Li Chemical engineering National University of Singapore __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com |
|
From: li j. <lj...@ya...> - 2005-07-25 02:35:03
|
Dear all, I am a new user of Towhee. I have compiled towhee under Linux and get the binary file. I want to try the examples in Example directory, but I don't know how to run those examples. I tried several command, like "towhee <towhee_input> towhee_output" or "towhee <towhee_input", but they don't work, with the error message: segementation fault. Could anybody kindly tell me the command or provide me the scritpt to run the software? Thanks in advance, Li Chemical engineering National University of Singapore --------------------------------- Start your day with Yahoo! - make it your home page |
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