Dear Justin, Again, I appreciate you. I learn much from you, feeling happy :)
Thanks a lot. Sincerely, Shima ----- Original Message ----- From: Justin A. Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Wednesday, June 27, 2012 10:10 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 1:35 PM, Shima Arasteh wrote: > I know it's much better to use a non-deprecated ff. But what could I do? I > have to regenerate the results of simulation done by gmx.ff . Aren't there > any solution to pass this step? I have no idea how to make gmx.ff work. I "solved" the issue by commenting out the line and seeing that no error resulted. This, of course, isn't an actual solution, just a debugging method. The force field defines its impropers in an odd way, and as such I don't know that there is a workaround. > > I PROMISE YOU AND ME TO REPEAT THE SIMULATION WHIT A MODERN FF AS SOON AS > POSSIBLE :) > The sooner, the better. This is an ancient force field, and vastly better parameter sets exist. -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 ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
