I will assume you found my earlier reply.
On Thu, Aug 22, 2013 at 2:58 PM, lara lara <lara.4884.gmail.com> wrote:
> Dear all
>
> Greetings !
>
> I am a new user of Glycam .
>
> I would like to build GAG molecule , for example
>
> the Alpha - iduronic acid 2 - O sulfate ( a single residue )
>
>
> for that I called the xleap of amber ,
>
> 1) I sourced the ff99 force field.
>
> 2)I sourced the GLYCAM_06h-12SB
>
> 3)i loaded the Sulfate.prep
>
> then i did as given in the sulphating residue in Glycam
>
> m = sequence { ROH 0uA}
>
> set m.2.O2 charge -0.463
>
> set m tail m.2.O2
>
> m = sequence { m SUL}
>
> charge m
>
>>Total unperturbed charge: -2.000000
>>Total perturbed charge: -2.000000
>
> I fixed the charge on the O2 atom as said , since the total charge should
> be an integer.
>
>
> when I tried to write the prm and top files
>
> it is giving the following error
> Checking Unit.
> WARNING: The unperturbed charge of the unit: -2.000000 is not zero.
>
> -- ignoring the warning.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Could not find bond parameter for: Oh - S
> Building angle parameters.
> Could not find angle parameter: Cg - Oh - S
> Could not find angle parameter: Oh - S - O2
> Could not find angle parameter: Oh - S - O2
> Could not find angle parameter: Oh - S - O2
> Building proper torsion parameters.
> ** No torsion terms for Cg-Cg-Oh-S
> ** No torsion terms for Cg-Cg-Oh-S
> ** No torsion terms for Cg-Oh-S-O2
> ** No torsion terms for Cg-Oh-S-O2
> ** No torsion terms for Cg-Oh-S-O2
> ** No torsion terms for H1-Cg-Oh-S
> Building improper torsion parameters.
> old PREP-specified impropers:
> total 1 improper torsion applied
> 0 improper torsions in old prep form
> Building H-Bond parameters.
> Parameter file was not saved
>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>
>
> can any one let me know what is wrong and is the sulfation done here is
> correct ?
>
>
> Thank you
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 22 2013 - 12:30:02 PDT
