Re: [AMBER] error with loading HEM parameters for constph redox calcuations

From: David A Case <>
Date: Wed, 29 May 2019 12:03:23 -0400

On Wed, May 29, 2019, Vaibhav Dixit wrote:

>I have tried setting the FE atom-type and bonding the Fe-S-Cys, but I'm
>unable to understand the correct syntax for specifying atoms/residues/unit.

>1W0E = loadpdb 1W0E_amber18.pdb
>bond 1W0E.A1501.43 1W0E.420.3408 #BOND CYS-S to HEM-FE

Syntax is unit.residuenumber.atomname

The residue number is the "Amber" residue number, starting at 1, and
incrementing by 1 for each new residue. For (perhaps not so good)
historical reasons, Amber has never made much use of chainId's, so
something like "A1501" won't be recognized. The atomname part would be
something like "FE" or "S".

The tleap "charge" command gives the total charge on a unit: e.g.

> charge GLU
Total unperturbed charge: -1.000000
Total perturbed charge: -1.000000

I know it can be hard to find things in the manual. For tleap, I find the
interactive help environment to be the most useful. Typing "help" shows
you that there is a "charge" command, and typing "help charge" shows you
how to use it.

...hope this helps....dac

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Received on Wed May 29 2019 - 09:30:03 PDT
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