AMBER Archive (2003)

Subject: protonate

From: S.Swaminathan (swamy_at_www.cdfd.org.in)
Date: Tue Apr 08 2003 - 14:14:50 CDT

When i look at the protonated pdb (.H) file.
I see that the output format is altered from that
of the standard pdb format in which the input
pdb file is specified.

i see that the 3rd column (atom name) is shifted
slightly to the left, when compared to the original
pdb file. Why is it so ? Can we avoid it ?
What happens to the last two columns of the input pdb?
(they are absent in the protonated output file).

Swaminathan

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S.Swaminathan
Technical Officer - Bioinformatics
Centre for DNA Fingerprinting & Diagnostics (CDFD)
ECIL Road, Nacharam,
Hyderabad - 500 076
Tel: 27151344,346 Extn. 1207/1208
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