Re: [AMBER] TUTORIAL A1: Protein that Contains Non-Standard Residues

From: FyD <>
Date: Tue, 27 Mar 2012 15:30:52 +0200

Dear Bala,

I send my answer to the q4md-fft & amber mailing lists as you posted
your email in both mailing lists.

Either you consider the copper atom as a Cu2+, or you consider the
charge of the copper atom delocalized on the amino acid ligands; this
means the charge value will not take an integer value and will be far
below 2.0.
1- If you consider Cu2+ i.e. with an integer 2+ charge you could adopt
two approaches
     1.1. you use ligands/amino-acids from the Amber force field
topology database (I would not use this approach)
     1.2. you recompute the charges for the entire complex; i.e. amino
acid ligands & metal forcing an integer charge value for the metal
(using a specific constraint during the charge fitting step)
2- If you consider the charge of the copper delocalized on the amino
acid ligands, you recompute the charges of the entire complex however
without any constraint on the metal center.

We have followed the approaches 1.2. and 2-; see projects in R.E.DD.B.
(the paper is now submitted)

Here, in these two approaches you need to extract the active site from
the protein (generally available in the PDB file format); this means
generate an intermediate molecular fragment for the active site; then
you will cap this active site to transform this intermediate fragment
into a whole molecule (a QM program does not recognize a molecular
fragment), which will be involved in charge derivation i.e. geometry
optimization and MEP computation by QM and then charge fitting using
the RESP program...
During the charge fitting step, specific charge constraints are used
for the capping groups to lead to the generation of charge values for
the input molecular fragment extracted from the protein. At the end
you load the FF library(ies) generated by R.E.D. in the LEaP program
with other FF libraries from the Amber force field topology database
to be able to match the protein in the PDB file format.

Once you have generated the capped active site in the PDB file format
you could use R.E.D. Server to automatize charge derivation for your
active site...

these are only generalities, you can ask as many questions as you wish
from here ;-)

regards, Francois

> I am trying to reproduce tutorial A1. In section two, it is shown how to
> use leap to create a new residue (for copper). I followed the same
> procedure as given in the tutorial. creating a unit called CUA - editing
> the copper atom to define type and charge - saving the library as cua.lib.
> After creating a new residue called CUA and saving the lib file, I quit the
> leap and then started it again. Then i tried to create a prmtop and crd
> files for copper but leap shows me the following error.

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Received on Tue Mar 27 2012 - 07:00:03 PDT
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