Re: [AMBER] creating parameters for a thioglycoside

From: <>
Date: Mon, 11 May 2020 12:27:48 +0200

Hello Karl,

Thank you very much for yor advices.

After some struggling, I managed to calculate the inpcrd and prmtop
parameters for the molecule.

As you suggested, Adjusting the atom types and inserting the missing
bond parameters in the frcmod files for the linkages worked. Also, the
MD simulation looks consistent with the experimental data.

Thanks a lot,


Karl Kirschner <> ha scritto:

> Hello Rosa,
> I'm guessing that you need to create these parameters by hand, such that
> the atom types for the two force fields are accounted for. I think the
> problem likes at the parmchk2 step, which doesn't cobble force-field
> together that have different atom types (e.g. gaff and Glycam06). For
> example, assuming that you are using gaff for the sulfur atom (e.g. s2),
> then you need a bond parameter that is called s2-Cg. A first approximation
> would be to take an equivalent parameter out of gaff.dat (of gaff2.dat) and
> rename the atom types. Another way to do this would be to generate some QM
> target potential energy curves, optimize the force-field parameters that
> are missing, and then validate them using some test molecules and
> experimental data. But that takes some time to do. Your molecule looks
> pretty rigid around the sulfur atom (i.e. three rings), where puckering
> would give you the most conformational flexibility. In this case, using the
> gaff-Glycam06 combination might be sufficient. But note that this isn't a
> "standard" procedure, so keep that in mind when you try to interpret the
> resulting data.
> Bests,
> Karl
> On Mon, May 4, 2020 at 6:59 PM <> wrote:
>> Good afternoon,
>> I need to run a MD simulation using a ligand which is a Sialyl T
>> antigen analogue.
>> The ligand is constituted by 0SA and 6LB which is connected to a five
>> member heterocyclic molecule.
>> The connection of Galactose to the organic moiety are a sulphur bridge
>> to C1 and a glycosidic likage to C2 (of Gal).
>> I followed amber tutorials and employed antechamber to build the
>> organic moiety,usig as input the .mol2 file of the structure to create
>> a .prepi file
>> I used the .prepi file to run parmchk2 and create the .frcmod file.
>> Then I ran tleap loading the .prepi and .frcmod files to create the
>> .inpcrd .prmtop parameters for the molecule and succeeded.
>> To connect the organic part to the 0SA-6LB part, I loaded the ffs, the
>> .prepi and .frcmod files and the pdb constituted by the digal and the
>> organic moiety in close proximity and used the bond command to connect
>> the two moieties.
>> I ran tleap to calculate the parms for the entire molecule and I got
>> FATAL error messages saying that leap could not find the bond, angle
>> and dihedral parameters for the S-C bond between the two moieties.
>> How could I solve the problem? Are there other ways to parametrize
>> this molecule?
>> Please find attached the PDB of the structure
>> Many thanks in advance,
>> Cordially,
>> Rosa
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Received on Mon May 11 2020 - 03:30:03 PDT
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