From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Tue Apr 11 2006 - 12:38:18 CDT
Hi,
You should have a look at the NAMD tutorial in order to understand what
psfgen is doing ( http://www.ks.uiuc.edu/Training/Tutorials/ ). The extra
atoms are hydrogens, generally not present in crystal structures (see the
X-ray Crystallography box at
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node6.html
)
Marcos
On Tue, 11 Apr 2006, snoze pa wrote:
> Hi,
> I have a general question about psfgen. When We use psfgen to create
> psf files, it add more atoms in the final pdb file, eg in case of ALA,
> the original system is
>
> ATOM 351 N ALA G 12 44.524 12.388 34.365 1.00 95.86 N
> ATOM 352 CA ALA G 12 43.995 12.940 35.608 1.00 96.87 C
> ATOM 353 C ALA G 12 45.097 13.350 36.586 1.00 97.26 C
> ATOM 354 O ALA G 12 44.942 13.202 37.800 1.00 97.93 O
> ATOM 355 CB ALA G 12 43.063 11.924 36.267 1.00 96.68 C
>
> How ever, After using psfgen it creates followiing
>
> ATOM 695 N ALA 12 44.524 12.388 34.365 1.00 0.00 P
> ATOM 696 HN ALA 12 44.484 11.392 34.286 0.00 0.00 P
> ATOM 697 CA ALA 12 43.995 12.940 35.608 1.00 0.00 P
> ATOM 698 HA ALA 12 43.422 13.836 35.399 0.00 0.00 P
> ATOM 699 CB ALA 12 43.063 11.924 36.267 1.00 0.00 P
> ATOM 700 HB1 ALA 12 42.237 11.668 35.569 0.00 0.00 P
> ATOM 701 HB2 ALA 12 43.606 10.985 36.513 0.00 0.00 P
> ATOM 702 HB3 ALA 12 42.612 12.327 37.199 0.00 0.00 P
> ATOM 703 C ALA 12 45.097 13.350 36.586 1.00 0.00 P
> ATOM 704 O ALA 12 44.942 13.202 37.800 1.00 0.00 P
>
> Any idea.
>
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