[gmx-users] Generating topology file

Alan alanwilter at gmail.com
Wed Nov 23 11:54:12 CET 2011

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,


On 23 November 2011 10:35, madhumita das <madhumita.bioinfo at 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
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Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588
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