AMBER Archive (2009)

Subject: [AMBER] RE: question about TUTORIAL A1

From: Ross Walker (
Date: Sun Jul 05 2009 - 21:29:38 CDT

Hi Zeinab.


I am copying this to the AMBER mailing list which is where such questions
should normally be posted. See for signup details.


A few questions. Are you sure this Calcium bonds to 7 atoms in amino acids?
This seems unlikely to me, are you sure it bonds to this much, with covalent
bonds? How are these formed?


I would start by looking in the literature to see if you can get parameters
for this. I would then as a first pass make this calcium a residue in its
own right with a charge of 2+. I would then build nonstandard versions of
the residues that bond to this, deleting the proton that is bound to the
atom that bonds to the Ca and then refit the charges on these amino acids.
You can then bond these using the bond command in leap and provide
parameters through a frcmod file. This will do as a first pass, following on
from this you might want to consider a complete refit of the bound ligands
and the Ca atom together.


Good luck,



From: zeinab bagheri []
Sent: Friday, July 03, 2009 8:24 AM
Subject: question about TUTORIAL A1


Dear Ross Walker
I read the TUTORIAL A1 ( Simulating a Solvated Protein that Contains
Non-Standard Residues) and simple version of this,
I want use the method was introduced in this tutorial.
the protein in my work have one structural Ca , which bonds to 7 atoms from
the 6 Amino Acids.

I don't know which of them I must selected as modified Amino Acid that Ca
should Add in its atoms.
is this very important?


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