Please keep all correspondence on the list.
Zhong Zheng wrote:
Yes.
Amber. Gromacs Version 4.0.2. It's compiled on my computer, macbook. I
followed standard procedure,nothing special.
The Amber force fields use their own special nomenclature, so N-terminal alanine
would actually be called NALA. You will have to modify your .pdb file to
correspond with Amber naming conventions before this step will complete properly.
-Justin
On Jan 14, 2009, at 2:28 PM, Justin A. Lemkul wrote:
Zhong Zheng wrote:
I tried this: pdb2gmx -f prot.pdb -ignh, not working
What I am using is : pdb2gmx -f prot.pdb -missing
Does the behavior occur when you process each chain separately?
Which force field are you using? Which version of Gromacs are you
using, and how was it compiled? I experienced the same behavior in
version 3.3.1, resulting from a broken Ubuntu package.
-Justin
On Jan 14, 2009, at 2:16 PM, Justin A. Lemkul wrote:
What is your exact pdb2gmx command line?
-Justin
Zhong Zheng wrote:
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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--
========================================
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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--
========================================
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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--
========================================
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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