See this:
http://glycam.ccrc.uga.edu/ccrc/pages/sulfation.html
On Thu, Aug 22, 2013 at 3:07 PM, lara lara <lara.4884.gmail.com> wrote:
> I got the reply ,
>
> I will look in to Glycam documentation
>
> thank you
>
>
> On Thu, Aug 22, 2013 at 3:03 PM, Lachele Foley <lf.list.gmail.com> wrote:
>
>> 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
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu Aug 22 2013 - 12:30:04 PDT
