On 5/14/12 11:19 AM, Shima Arasteh wrote:
Dear gmx users,
I changed the aminoacids.rtp file recently.
Now, when I run pdb2gmx, I get the fatal error:
atom H is missing in residue For 0 in the pdb file
You might need to add atom H to the hydrogen database of building block For
in the file aminoacids.hdb
-Is it may as a result of some problems in .rtp file?
The error states that an H atom is specified in the .rtp entry but is not
present in the .pdb file. They two must match. In the case of H atoms, they
can be rebuilt if a suitable .hdb entry exists. See the manual.
-May I use -missing option and get a appropriate output? As I see in manual, I
can use this option when I want to generate specialized topologies for amino
acid-like molecules to take advantage of .rtp entries. The part which I entered
in .rtp file is a formyl as the N-terminal for the protein. I guess I can use
-missing option, Can't I?
There are very limited cases where the -missing option should be used. This is
not one of them.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
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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