Re: [AMBER] Modified cysteine parameters

From: Dr. Anselm Horn <>
Date: Mon, 20 Jul 2020 10:46:00 +0200

Dear krishnendu sinha,

> I was trying to generate parameters for modified cysteine residue (cysteine
> geranyl) In my protein it is the C terminal residue. For generating the
> parameter I have followed the B5 tutorial ( Green Fluorescent Protein). I
> am attaching all the necessary file. WT.pdb the pdb file after running
> pdb4amber. CGR is the name of the modified residue.

the problem seems to be that you provide parameters for a mid-chain CGR
residue, i.e. having -NH-CA(H)(R)-C(=0)- topology, but your system
WT.pdb contains an C-terminal CGR residue with -NH-CA(H)(R)-C(O)2:
in your input pdb file, an OXT atom occurs, which is not present in your
parameter template CGR.prepin - and thus leap gives an error message.
(There is no automagic leap mechanism that creates parameters for
terminal residues from mid-chain ones; technically, these are different

Thus, you have to provide/create specific parameters for the C-terminal
species of CGR, if that residue is really the terminal one in your system.

You may, however, re-use most of you parameters from the mid-chain
parameterization (i.e. most atom types, bond/angle/... parameters), but
you have to generate a different CGR.prepin template file, which
includes OXT, and redo the atomic charge parameterization due to the
different electrostatic situation with the negative charge at the
carboxylate group.

Hope that helps.

Best regards,


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Received on Mon Jul 20 2020 - 02:00:03 PDT
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