hi
Thanks for your reply. I tried -ignh and it doesn't help. I understand
-missing is bad but I made sure the only missing atoms the program
complains are the first residue in each three chains.
I am using a crystal structure. However the warning messages are
only for the first residue in each chain.
Zhong
On Jan 14, 2009, at 1:59 PM, Justin A. Lemkul wrote:
Zhong Zheng wrote:
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?
Use -ignh to allow the relevant .hdb file to add the appropriate
hydrogens. The problem is that, without -ignh, pdb2gmx expects all
atoms (including H) to be present in the .pdb file. If you are
using a crystal structure, this requirement will not be satisfied.
Likely pdb2gmx does not complain about the C-terminus because it is
unprotonated, or otherwise the program exits after finding a missing
N-terminal hydrogen.
As an aside, using -missing is generally a very bad idea, unless you
have a very specific (and anticipated!) reason to use it.
-Justin
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 <http://scratchpad.wikia.com/wiki/MCCE
>
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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