Dear Dr.justin Actually by doing this we are using two different force fields in one simulation. I had done it before and the result was that I discussed before in gmx-users(LINCS Error,Exploding system,Bad contacts between atoms) Then,this approch seems to doesn't work about my system.
Then I want to find charges and charge groups for gromos 43A1 and replace them for my drug(to edit PRODRG file manually) and work totally in gromos 43A1. Unfortunately I can't obtain these parameter. Please let me have if you have it. Can I use some Ab Initio software for determining partial charges of my drug? for example ABINIT or Gaussian! Thanks in advance On Sat, Jan 22, 2011 at 8:03 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > mohsen ramezanpour wrote: > >> Ok >> then,I can use PRODRG server to generate .top and .gro files for drug. >> since it's reported charges are not very accurate ,we can replace all >> charges completely with them in 53A6(if was present). >> But it means we are working in 53A6 force field. >> then,we must generate .top and .gro files for our protein with 53A6 too. >> and work completely with 53A6. >> Am i right? >> thanks in advance >> > > That sounds like a reasonable approach. Be sure to validate the drug > topology. In my experience, this procedure is pretty good, but you always > have to convince reviewers... > > -Justin > > >> On Sat, Jan 22, 2011 at 4:43 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> mohsen ramezanpour wrote: >> >> Dear Justin >> >> I read your articles about PRODRG server,they were very useful. >> But I have a question: >> are charges of functional groups and generally other atom groups >> the same in all force fields? >> Because you have modified charges of your molecules by Gromos96 >> 53A6 while prodrg server is generating topology files in 43A1. >> I want to know can I replace charges from gromos 53A6 or other >> forcefields? >> thanks in advance >> >> >> Charges are not the same between force fields. We did our study >> with 43A1 since that is what PRODRG purports to produce. I would >> say that our recommendations carry to other Gromos force fields, as >> well, but don't take charges from 43A1 and apply them to 53A6. Be >> consistent within the force field. >> >> The atom types produced by PRODRG are largely shared between 43A1 >> and 53A6, so if you *completely* replace all charges with those from >> 53A6, you should have a topology that is compatible with 53A6. >> >> -Justin >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> 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 gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 > 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 >
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