AMBER Archive (2009)

Subject: Re: [AMBER] ambpdb is changing atom names, a feature or bug?

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Fri Jan 09 2009 - 11:53:23 CST

Not only does H3 change into 2H, but it makes for duplicate 2H atoms.
This really seems like a bug. Please let us know if using the flag Dave
Case indicated fixes the problem (even if it does I think there's still
a bug).

Bill

> in prmtop file one has
> %FLAG ATOM_NAME
> %FORMAT(20a4)
> C6 H7 H8 H9 C5 H5 H6 C4 H3 H4 N C H N1 C3 H10 H11 H12 C1 H1
> C2 H2
>
> and in the resulting pdb file (test.pdb)
> REMARK
> ...
> ATOM 8 C4 PM2 1 -1.537 -0.142 -0.665 -0.1718 1.700
> ATOM 9 2H PM2 1 -1.831 0.578 -1.415 0.1197 1.300
> ...
> ATOM 21 C2 PM2 1 0.440 1.349 -0.090 -0.2547 1.700
> ATOM 22 2H PM2 1 -0.134 2.249 -0.118 0.2818 1.500

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