Re: Re: 1-4scaling for glycosylated protein using AMBER/GLYCAM FF in NAMD

From: Lachele Foley (
Date: Tue Mar 17 2015 - 21:46:19 CDT

You have to find an experimental measurement to which you can compare.
NMR is often good. Be sure to calculate the NMR measurable itself and
not compare to any reported populations that were derived from the
measurements. You need to do this no matter which force field you
choose. I have not used NAMD in this manner, so I don't know what the
behaviors might be. Perhaps some others here will have opinions on

On Tue, Mar 17, 2015 at 10:18 PM, clarkzhy <> wrote:
> Thanks for your reply.
> You are right that glycan's conformation could be affected after using
> protein's scaling factors.
> Do you have any experience about this kind of effect? How to judge that
> these effect is not fatal for the large time-scale (~us) simulation results?
> Or, use CHARMM36 FF instead?
> ________________________________
> clarkzhy
> From: Lachele Foley
> Date: 2015-03-18 10:15
> To: Namd Mailing List; clarkzhy
> Subject: Re: namd-l: 1-4scaling for glycosylated protein using AMBER/GLYCAM
> FF in NAMD
> If it isn't possible to use different scaling factors for the
> different parts of the simulation, we recommend using the protein's
> scaling factors. There will be some impact on the glycan's
> conformations. As always, validate your model!
> On Tue, Mar 17, 2015 at 9:33 PM, clarkzhy <> wrote:
>> Dear all,
>> I am confused on how to set 1-4 scaling factors (SCEE/SCNB) when using
>> NAMD and Amber/Glycam06 to simulate the glycosylated protein.
>> Amber FF requires SCEE=1.2/SCNB=2 (1-4scaling=0.833333/scnb=2.0 in NAMD)
>> , but Glycam06 requires 1 for both factors. In top file generated by tleap
>> (Ambertools14) , there are two sections to handle this:"SCEE_SCALE_FACTOR"
>> and "SCNB_SCALE_FACTOR"。But in NAMD2.9, these two section are ignored.
>> "Warning: Skipping SCEE_SCALE_FACTOR in parm file while seeking SOLTY.
>> Warning: Skipping SCNB_SCALE_FACTOR in parm file while seeking SOLTY."
>> So, this means NAMD deal with all 1-4 interaction using the same scaling
>> factors defined by 1-4scaling/scnb=2.0, am I right?
>> Can anybody have a good way to handle this 1-4scaling to simulate the
>> glycosylated protein using Amber/Glycam06 FF in NAMD?
>> --------------
>> clarkzhy
> --
> :-) Lachele
> Lachele Foley
> Athens, GA USA

:-) Lachele
Lachele Foley
Athens, GA USA

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