Zhong Zheng wrote:
You mean rename ALA as NALA in the .pdb for the n-terminus Ala? If so, i
tried already and still not working.
Yes, you would have to rename all N-terminal ALA as NALA, as well as specify the
correct Amber residue names for all other amino acids in your structure (i.e.,
C-terminal residues, histidines, etc). An easy way might be to process your
.pdb with xLeap (now free as part of AmberTools), and use the output .pdb as
your input into pdb2gmx.
Have you carefully followed all instructions here:
http://chemistry.csulb.edu/ffamber/#usage
Have you updated your aminoacids.dat appropriately (see above link)?
-Justin
On Jan 14, 2009, at 2:38 PM, Justin A. Lemkul wrote:
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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Virginia Tech
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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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========================================
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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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========================================
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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