[AMBER] GLYCAM and scaling of electrostatic and nonbonded interactions

From: Jordi Bujons <jordi.bujons.iqac.csic.es>
Date: Thu, 11 Jun 2020 18:17:29 +0200



I am trying to simulate a sulfated heparin model and its interaction with a
series of cationic polyamines. I prepared an heparin decamer using
GLYCAM-web, had the polyamines modeled and calculated their resp charges
using Gaussian, and built the heparin-polyamine systems with tleap using
glycam_06j-1 and gaff2 as forcefields. Everything looked good and I could
run 20ns MD without problems. Now, my doubts came when I read the following
on the glycam section of the amber 2017 reference manual:


3.3.4. Scaling of electrostatic and nonbonded interactions

As in previous versions of GLYCAM,[2] the parameters were derived for use
without scaling 1-4 non-bonded

and electrostatic interactions. Thus, in sander, pmemd, and so on, the
simulation parameters scnb and scee should

typically be set to unity. We have shown that this is essential in order to
properly treat internal hydrogen bonds,

particularly those associated with the hydroxymethyl group, and to correctly
reproduce the rotamer populations

for the C5-C6 bond.[57] Beginning with Amber 11, it is now possible to
employ mixed scaling of the scnb and

scee parameters. Anyone wishing to simulate systems containing both
carbohydrates and proteins should use the

new mixed scaling capability. To do this, any scaling factors that differ
from the default must be included in the

parameter file. Beginning with the GLYCAM_06g parameter file shipped with
Amber 11, these factors are already

included. Anyone wishing to employ earlier parameter sets must modify the


Should I set parameters scnb and scee = 1 to run these simulations or are
these factors already included in the parameter files, as suggested in the
last two lines of the above paragraph? Are there any other special settings
that I should take into account? Furthermore, I wonder if it makes sense to
try to use mmpbsa.py to try to estimate binding affinities of the polyamines
to heparin. Any suggestions will be highly appreciated.







Jordi Bujons, PhD
Dept. of Biological Chemistry (QB)
Institute of Advanced Chemistry of Catalonia (IQAC)
National Research Council of Spain (CSIC)
Address: Jordi Girona 18-26, 08034 Barcelona, Spain
Phone: <tel:%2B34%20934006100%20ext.%201291> +34 934006100 ext. 1291
FAX: <tel:%2B34%20932045904> +34 932045904
 <mailto:jordi.bujons.iqac.csic.es> jordi.bujons.iqac.csic.es
 <http://www.iqac.csic.es> http://www.iqac.csic.es


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Received on Thu Jun 11 2020 - 09:30:03 PDT
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