ambpdb and protonate in AMBER7

From: Francisco Blanco <>
Date: Thu, 17 Apr 2003 13:38:29 +0200 (CEST)

I am trying to write a pdb after an energy minimization Using AMBER7 under
LINUX RH7.3. So far I have been unable to write down a pdb compliant with
the brookhaven format. I also fail to properly read the amber generated
pdb with MOLMOL, which reads other NMR related formats like DYANA.

This are my findings:


It seems that the option -bres does not work well, it wipes out the atom
name filed (as does the -aatm option).


1. The -b option (described in the manual) does not exist, although it
appears to be unnecessary with the PROTON_INFO library

2. Even though the PROTON_INFO.Brook file contains the brokhaven atom
names (like 1HD1, 2HD1, 3HD1 protons of one of the leucine methyls),
protonate does not make its job and writes 11HD,12HD, 13HD. In addition,
protonate writes the "H" atom label in the 15th column (instead of using
the 14th column, as done for heavy atoms) and does funny things with the
aromatic ring protons (for example, "1HD PHE" is written as " 1 HD PHE")
and the HG1 of threonines (it writes "1 HG THR").

Is there a way around to have a clean brookhaven pdb formatted file?


Francisco Blanco
NMR group, Structural and Computational Biology Programme
Centro Nacional de Investigaciones Oncológicas
Melchor Fernández Almagro 3, 28029 Madrid, Spain
Phone: 91 2246983/Fax: 91 2246976   
Received on Thu Apr 17 2003 - 12:53:01 PDT
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