[AMBER] creating parameters for a thioglycoside

From: <rosaester.forgione.unina.it>
Date: Mon, 04 May 2020 18:59:39 +0200

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,



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Received on Mon May 04 2020 - 10:00:02 PDT
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