I am sorry, but because antechamber will only work with these atoms: C, N, O, S, P, H, F, Cl, Br and I, so acype won't work for Hg.
A "hack" would be to replace Hg by another allowed element. But this is only to give you a hint of what topology and parameters might look like. Then you have to work hard in literature to find parameters and likely make use of RED for getting a more quantum mechanics approach for your parameters and charges. Good luck, Alan On 23 November 2011 10:35, madhumita das <madhumita.bioi...@gmail.com>wrote: > Hi GROMACS users, > > I have used acpype.py to convert parameter and topology file from > amber to gromacs but some of the parameters (angle and > dihedral)regarding a particular residue having mercury in it was not > generating,please help. > Thanks > in advance. > > Madhumita Das > > -- > 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, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588
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