AMBER Archive (2009)

Subject: Re: [AMBER] loadpdb atom type

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue May 19 2009 - 13:19:44 CDT

On Tue, May 19, 2009, Mark M Huntress wrote:

> Hi, I have a pdb that was saved on VMD, and AMBER doesn't want to load it right.
>
> It creates about 400 new hydrogens, because it apparently cannot recognize the hydrogens that are already there.
>

This came up just a few days ago. VMD is writing an incorrect pdb
file. In principle, Amber ought to handle it (especially since VMD works
hard to read in various Amber file formats), but tleap doesn't do that.

A workaround is to reformat the VMD pdb file, perhaps even removing all
hydrogens.

>
> ATOM 2146 N ARG A 136 -15.329 -2.598 -9.210 1.00 0.00
> ATOM 2147 H ARG A 136 -15.332 -3.533 -9.614 1.00 0.00
> ATOM 2148 CA ARG A 136 -15.497 -1.426 -10.034 1.00 0.00
> ATOM 2149 HA ARG A 136 -14.896 -0.566 -9.736 1.00 0.00
> ATOM 2150 CB ARG A 136 -15.344 -1.704 -11.501 1.00 0.00
> ATOM 2151 2HB ARG A 136 -15.675 -2.780 -11.830 1.00 0.00
> ATOM 2152 3HB ARG A 136 -15.854 -0.894 -12.075 1.00 0.00
             ^^^^^^

Above two lines are incorrect: the atom name should be shifted left by one
column.

...dac

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