Hi, Not sure exactly what you plan to simulate but here are a couple of potential pitfalls:
Does acpype call amb2gmx.pl or is it new code that converts? If it is a amb2gmx.pl call I'd check the torsions on the NAc group if you have one. They didn't get translated when I used it. When using amber ports be careful about using default index groups like "protein" or "C alpha" as they won't contain atoms from residues like LYP that are different in the ports. Also you'll want to set fudge to 1.0 in the amber99sb.itp or where it is set (can't check this atm) if simulating the sugar alone. Its due to differences in the way amber and glycam are parametrized. (If you are interested it is differences in 1-4 scaling). There may be other issues I'm not aware of yet. :) All the best, Oliver On 23 December 2010 18:13, Alan Wilter Sousa da Silva <awil...@ebi.ac.uk>wrote: > Have a look at acpype.googlecode.com > > Alan > > 2010/12/23 gromacs564 <gromacs...@126.com> > >> >> Hi , >> >> I have obtained some files(.top,.crd,.pdb) about disaccharide via >> glycam web(they are glycam06 force field,included in AMBER) , but cannot >> converted this amber files to gromacs files format. >> >> >> Can anyone help me to convert this (amber) files to gromacs input >> files(top or itp,gro).? >> >> Many thanks! >> >> >> >> >> >> >> >> >> -- >> 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 >> > > > > -- > Alan Wilter SOUSA da SILVA, D.Sc. > Bioinformatician, UniProt - PANDA, EBI-EMBL > CB10 1SD, Hinxton, Cambridge, UK > +44 1223 49 4588 > > > -- > 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 >
-- 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
