Hello,
I am trying to convert a pdb from CHARMM to AMBER, to run a simulation. This pdb contains glycans, some of which contain sialic acid. When I load this pdb into tleap, I see missing angle parameters:
Error: Could not find angle parameter for atom types: Cy - Cg - Os
However, the $AMBERHOME/dat/leap/parm/GLYCAM_06j.dat file contains these parameters:
Os-Cg-Cg 70.00 108.50 Methoxyethane (Ethylmethyl ether)
Os-Cy-Cg 70.00 108.50 Methoxyethane (Ethylmethyl ether) - for sialic acid only!
1) I am always wary about changing parameters; is it acceptable to add this new parameter for these atom types to $AMBERHOME/dat/leap/parm/GLYCAM_06j.dat?
Os-Cg-Cy 70.00 108.50
If not, how would I go about getting parameters for Os-Cg-Cy?
2) I manage the AMBER installation for my organization; are there best practices for modifying parameter files like this that others will use?
Thanks in advance!
Best,
Christian
Christian Seitz
PhD, Dept. of Computer Science | UChicago
cgseitz.uchicago.edu<mailto:cgseitz.uchicago.edu>
[www.linkedin.com/in/christianseitz21]<
http://www.linkedin.com/in/christianseitz21>
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Received on Mon Jul 07 2025 - 13:30:02 PDT
