Re: [AMBER] Amber B5 tutorial

From: David A Case <>
Date: Fri, 12 Aug 2016 15:22:25 -0400

On Fri, Aug 12, 2016, Chitrak Gupta wrote:
> Thank you for your response and referring me to the B5 tutorial.
> What is not clear to me is how I obtain a ccif file for my new residue.

Ah...good point: if your modified amino acid is not in the components.cif
file provided by the RCSB, you'll have to proceed by a different method:
Create a pdb file with all hydrogens for your residue plus capping residues,
convert that to .ac format with antechamber, and proceed as in the tutorial.

In practice, the R.E.D. tools may be better set up to do this sort of thing
(not sure, since I haven't had time to learn R.E.D. myself.

...good luck...dac

Note: if you want to check the components.cif file to see if your modification
is one that is present in the PDB, you can download the "Chemical Components
Library" from look under the "Deposit" Menu item.

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Received on Fri Aug 12 2016 - 12:30:02 PDT
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