[gmx-users] atom H is missing in the first residue in a chain

Zhong Zheng zhozheng at gmail.com
Wed Jan 14 19:43:56 CET 2009

Hi all

I am running Gromacs on a three-chain protein. The program complains  
about "atom H is missing in residue ALA 1 in the pdb file, You might  
need to add atom H to the hydrogen database of residue ALA in the file  
ff???.hdb (see the manual)". It's a warning message. I can use the  
option -missing to ignore it. However I would like to understand this.  
It's always the first residue in the chain. So I am thinking this is  
because they are the n-terminus. Then why no complain about c- 
terminus? How can I fix this?

Thanks a lot.

Zhong Zheng
Ph.D candidate
Physics Dept., City College-CUNY
Marshak Science Building J-419 ,
160 Convent Ave,
New York, NY 10031 USA
Tel: (212)650-6079
MCCE wiki: scratchpad.wikia.com/wiki/MCCE

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