[AMBER] Parametarization error

From: senal dinuka <senal.ichemc.edu.lk>
Date: Thu, 18 Oct 2018 10:04:09 +0530

I have been trying to generate prmtop and inpcrd files for the below
mentioned receptor/ligand complex. The ligand is a TS structure hence the
weird bond lengths. I was told to use GLYCAM for the sugar portion and
separate frcmod for the cyanogenic part of the ligand since GLYCAM doesnt
offer parameters for the later. Hence I generated a l1.frcmod with bcc
charge scheme through antechamber and parmchk modules with default options.
frcmod seem to be lack in bond and angle properties. And thus the leap
results in error I assumed. I appreciate your guidance regarding the matter.

Thank you
P.S I have attached the complex, ligand as well as frcmod and leap script I
used


-- 
D L Senal Dinuka
Grad.Chem., A.I.Chem.C.
Research Assistant
College of Chemical Sciences
Institute of Chemistry Ceylon
Rajagiriya
Sri Lanka
+94 77 627 4678







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Received on Wed Oct 17 2018 - 22:00:02 PDT
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