Re: [AMBER] Error during Adding Fragment(about MCPB )

From: David A Case <>
Date: Thu, 19 Mar 2015 08:11:34 -0400

On Thu, Mar 19, 2015, wjli wrote:
> In amber,there are residue templates that you can find through
> ‘list’ command.My questions are:

> 1.what's the residue name for Arginine protonated?(ARG and
> what?)Similarly,for Tyrosine deprotonated(TYR and what)?

If by "arginine protonated" you mean a +1 side chain charge, that is "ARG".
No other alternates are provided in the standard library. Similarly, we
don't have deprotoned tyrosine in the standard library. Hydroxyl ions are
also not in the standard library.

If the variant you want is in the PDB "components" library (components.cif),
you can load these into antechamber (use the "-fi ccif" flag), and create a
unit in the usual way. Many useful entities are also in the R.E.D. database.
See also the constant pH chapter of the Amber Reference Manual.


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Received on Thu Mar 19 2015 - 05:30:03 PDT
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