I have a question related to charmm. Does charmm have a name/structure chart for all the parametrized molecules? I want to borrow some parameters info from those molecules but often I can't quickly figure out what they are. Ming
On Jan 18, 2018 8:18 AM, "MD" <refm...@gmail.com> wrote: > Coolbeans! Thank you Justin :) > Ming > > On Jan 18, 2018 7:54 AM, "Justin Lemkul" <jalem...@vt.edu> wrote: > >> >> >> On 1/18/18 7:51 AM, MD wrote: >> >>> On Thu, Jan 18, 2018 at 7:43 AM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>>> On 1/17/18 6:11 PM, Mark Abraham wrote: >>>> >>>> Hi, >>>>> >>>>> If you poke your finger into something, it isn't going to stay flat. >>>>> :-) >>>>> >>>>> And to add on to this, in the CHARMM parametrization protocol, the >>>> first >>>> step is always an in vacuo geometry optimization (QM vs. MM comparison) >>>> to >>>> make sure the topology is sensible. If that doesn't check out, there are >>>> problems that can be easily spotted before subjecting the new residue to >>>> any other complicating factors like water and other parts of the >>>> protein. >>>> >>>> -Justin >>>> >>>> Thank you Justin. What would you look at to make a judgement to see if >>> the topology is sensible after the vacuo geometry optimization? Or as >>> long >>> as there were no errors or bad notes along the run it should be good? >>> >> >> You look at the structure to see if it is sensible (and here, sensible is >> defined as properly reproducing QM-optimized geometries and/or known >> high-resolution experimental geometries - start with QM and compare against >> empirical evidence later). >> >> The absence of errors or notes when executing grompp tells you precisely >> nothing about the integrity of the physical model; it only tells you if >> you've forgotten to do something. I can populate every parameter field with >> absolute garbage and grompp will happily carry on preparing my doomed >> simulation :) >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Virginia Tech Department of Biochemistry >> >> 303 Engel Hall >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalem...@vt.edu | (540) 231-3129 >> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >> >> ================================================== >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support >> /Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.