That is correct. You might also see the section on building a
glycoprotein in the latest AmberTools manual for more detailed
information.
On Tue, Nov 30, 2010 at 9:06 PM, Emmanuel Baribefe Naziga
<baribefe.gmail.com> wrote:
> I think if you use sleap and issue the "set default write14scale on"
> command, leap will write the correct scaling for each part of your system in
> the topology file. However, you will need Amber 11 or PMEMD in AMBER 10 to
> use this topology file with different scaling factors.
>
> All the best,
>
> Emmanuel.
>
> On Tue, Nov 30, 2010 at 6:55 PM, Lishan Yao <yaolisha.msu.edu> wrote:
>
>> Dear Amber users:
>> We try to set up a md simulation for a protein sugar complex. We plan
>> to use amber ff99sb force field for the protein and GLYCAM force field for
>> the sugar. In ff98sb force field scee is set to 1.2 and scnb is set to 2.0,
>> but in GLYCAM scee = scnb = 1.0. My question is that how this is handled in
>> amber? Are the paramters set differently and saved in the topology?
>>
>> Best,
>> Lishan
>>
>>
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>>
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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Tue Nov 30 2010 - 20:00:02 PST
