Hi Lachele,
Thanks for your kindly reply！
Yes, there is a disulfide-type link(-CH2-S-S-CH2-) in my micelle molecule. Do you mean that this is not supported in the GLYCAM force field? And I need to use protein force fields and GAFF?
If I still want to use GLYCAM force field, how could I work out parameters by myself?
All the best,
Meng Wu
------------------------------
From: Lachele Foley <lf.list.gmail.com>
GLYCAM supports two varieties of sulfur atom. The following lines are from
the file $AMBERHOME/dat/leap/parm/GLYCAM_06j.dat :
S 32.06 sulphur in sulphates
Sm 32.06 sulfane carbohydrate linkage
(-CH2-S-CH2-)
I see in your leap output a bond for sulfur to sulfur - is this a
disulfide-type link? Do you expect such a bond to be present? If so, you
might be able to use the disulfide sulfur from the protein force fields,
but read the next bit.
If your sulfur doesn't fall neatly into one of the already-parameterized
categories, you might need to work out parameters for it rather than try to
just repurpose parameters for other sulfur atom types. GAFF is an approach
that sometimes works quite well for these situations. Whatever you do, if
your system is different, you need to validate the model before using it.
On Fri, Jul 21, 2017 at 8:17 AM, Meng Wu <wumeng.shanghaitech.edu.cn> wrote:
> Dear All,
>
> I would like to simulate a micelle in the water with Amber16, and there
> is a sulfur atom(S) in my micelle molecules. When I used leap and sourced
> leaprc.GLYCAM_06j_1, I got these errors:
> > check DSM
> Checking 'DSM'....
> Checking parameters for unit 'DSM'.
> Checking for bond parameters.
> Could not find bond parameter for: Cg - Ss
> Could not find bond parameter for: Ss - Ss
> Could not find bond parameter for: Ss - Cg
> Checking for angle parameters.
> Could not find angle parameter: Cg - Cg - Ss
> Could not find angle parameter: Cg - Ss - Ss
> Could not find angle parameter: Ss - Cg - H1
> Could not find angle parameter: Ss - Cg - H1
> Could not find angle parameter: Ss - Ss - Cg
> Could not find angle parameter: Ss - Cg - Cg
> Could not find angle parameter: Ss - Cg - H1
> Could not find angle parameter: Ss - Cg - H1
> There are missing parameters.
> Unit is OK.
>
> ?Ss? is the sulfur atom in the .mol2 file of a single micelle
> molecule(.mol2 file generated by antechamber). Does it mean the GLYCAM
> force field not support the sulfur atom type? If yes, how could I add it or
> other ways to fix it?
>
> Any suggestions would be greatly appreciated. Thank you in advance!
>
> All the best,
> Wu Meng
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Sun Jul 23 2017 - 04:30:02 PDT
