I was just able to get it to work.
These probably won't stop your build from working, but might:
1. Just for completeness, try using the SO3 residue shipped with
06h-12SB. We changed the name... and I keep hoping we'll have a new
website soon, but I'll update the doc.
2. You probably want to use ff12SB if you're going to source our 12SB
leaprc, particularly if you plan to attach to a protein/amino-acid.
More importantly:
3. If you want to attach a sulfate to the 2 position, you need 2uA,
not 0uA. You need to use the residue that has open valences wherever
you want to attach a sulfate -- plus any open valences needed to
attach other sugar residues.
4. Be sure that your leaprc is calling all the local files needed for
GLYCAM with 12SB. Also make sure you downloaded them.
On Thu, Aug 22, 2013 at 2:29 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 her 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
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Received on Thu Aug 22 2013 - 12:00:04 PDT
