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

From: clarkzhy (clarkzhy_at_foxmail.com)
Date: Tue Mar 17 2015 - 20:33:41 CDT

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"ĄŁBut 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?


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