Well, allow me this suggestion. Consider using http://q4md-forcefieldtools.org/ to get the right charges, then update these charges in the mol2 file and run acpype with “-c user” option. For a quick test, you can use “-c gas”, which would give you charges via gasteiger method.
Alan On 5 January 2014 22:07, Jonathan Saboury <jsab...@gmail.com> wrote: > I have this molecule I want to simulate: > http://pastebin.com/raw.php?i=7bsWKjU3 > > I have tried using acpype on the whole thing to obtain the needed .itp and > .gro, but it takes a couple days to finish and I get errors because I do > not have enough memory. > > I was wondering if splitting this molecule into parts, much like how > proteins are split into amino acid sections, would be a feasible way to > simulate this molecule. I haven't seen any tutorials on this, so not sure. > > I could split the molecule into the bowl shapes, the n-hexanes, and the > n-pentane linker. Or if that would not be the correct way, how would you do > it? > > My question is how would the input sections deal with the bonds between > sections? For example, if I had a ethane and wanted to split it into two > methyl pieces, would I make the input .pdb's as CH3's? I.E.: > http://pastebin.com/raw.php?i=jhwcYbAM > > And more importantly, how would I link these together in the .gro file? > (assuming it is the .gro file) > > Thank you, your help is very much appreciated! > > -Jonathan > -- > 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. > -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 -- 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.