[gmx-users] atom H is missing in the first residue in a chain
zhozheng at gmail.com
Wed Jan 14 20:13:24 CET 2009
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.
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.
>> 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
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