Dear, The top file downloaded from PRODRG did not consist of [atomtypes]. Please tell me how can I add and use this function?
Best regards, Cuong On 15 October 2012 16:43, Peter C. Lai <[email protected]> wrote: > Is there no [atomtypes] section in the top file? > > On 2012-10-15 03:53:54PM +0800, cuong nguyen wrote: > > Thanks for you email. > > I already had the .gro and .top files from PRODRG. Now I want to > reproduce > > these files following the LJ parameters in a published paper (charge, > sigma > > and epsilon values). I can change the charge in the top file, yet I do > not > > know how to change sigma and epsilon values. > > > > Best regards, > > > > Cuong > > > > On 15 October 2012 13:57, Peter C. Lai <[email protected]> wrote: > > > > > It's hard to understand your question. What do you mean by "reference > > > parameters"? You said you already obtained a .gro and .top from PRODRG, > > > which > > > uses the gromos 43a1 forcefield to derive the parameters, so if you > need > > > to change the LJ parameters, edit the top file it gave you. > > > > > > If you want to reproduce the results of a published paper, you should > use > > > the > > > forcefield and parameters specified in that paper and contact the > author(s) > > > if more details are needed. > > > > > > On 2012-10-15 10:42:57AM +0800, cuong nguyen wrote: > > > > Thank you very much for your email, Justin. > > > > in case I want to use the reference parameters, which force-field and > > > what > > > > should I do to get the .gro and .top files for this molecule? > > > > > > > > Best regards, > > > > > > > > Cuong > > > > > > > > > > > > On 12 October 2012 21:14, Justin Lemkul <[email protected]> wrote: > > > > > > > > > > > > > > > > > > > On 10/12/12 8:04 AM, cuong nguyen wrote: > > > > > > > > > >> Dear Gromacs Users, > > > > >> > > > > >> I got the .gro and .top files of 1-octanol downloaded from PRODRG > > > website. > > > > >> Please let me know if I can change charge, epsilon and sigma of > the > > > > >> molecule as written in a paper? and How to do? > > > > >> > > > > >> > > > > > Atom types from PRODRG rarely, if ever, need changing. Charges > can be > > > > > taken first by chemical homology (group-based approach that makes > > > Gromos > > > > > force fields convenient) and then by calculating the charges > yourself. > > > For > > > > > 1-octanol, it should be very straightforward to obtain parameters, > zero > > > > > charges on all the C atoms except for the one in the alocohol, then > > > > > standard alcohol charges for the C-O-H. Whether or not those > > > parameters > > > > > are sufficiently accurate is up to you to decide, but that's the > > > approach > > > > > one would take with this particular force field. > > > > > > > > > > -Justin > > > > > > > > > > -- > > > > > ==============================**========== > > > > > > > > > > Justin A. Lemkul, Ph.D. > > > > > Research Scientist > > > > > Department of Biochemistry > > > > > Virginia Tech > > > > > Blacksburg, VA > > > > > jalemkul[at]vt.edu | (540) 231-9080 > > > > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin< > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > > > > > > > > > ==============================**========== > > > > > -- > > > > > gmx-users mailing list [email protected] > > > > > http://lists.gromacs.org/**mailman/listinfo/gmx-users< > > > http://lists.gromacs.org/mailman/listinfo/gmx-users> > > > > > * Please search the archive at http://www.gromacs.org/** > > > > > Support/Mailing_Lists/Search< > > > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting! > > > > > * Please don't post (un)subscribe requests to the list. Use the www > > > > > interface or send it to [email protected]. > > > > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< > > > http://www.gromacs.org/Support/Mailing_Lists> > > > > > > > > > -- > > > > gmx-users mailing list [email protected] > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > > * Please don't post (un)subscribe requests to the list. Use the > > > > www interface or send it to [email protected]. > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > > > ================================================================== > > > Peter C. Lai | University of Alabama-Birmingham > > > Programmer/Analyst | KAUL 752A > > > Genetics, Div. of Research | 705 South 20th Street > > > [email protected] | Birmingham AL 35294-4461 > > > (205) 690-0808 | > > > ================================================================== > > > > > > -- > > > gmx-users mailing list [email protected] > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > * Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to [email protected]. > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [email protected]. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > ================================================================== > Peter C. Lai | University of Alabama-Birmingham > Programmer/Analyst | KAUL 752A > Genetics, Div. of Research | 705 South 20th Street > [email protected] | Birmingham AL 35294-4461 > (205) 690-0808 | > ================================================================== > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
