Thanks Justin. I fixed it this time. I basically renamed the terminal
residues. The reason it didn't work last time is probably because some
format problem. Thanks again.
On Jan 14, 2009, at 2:50 PM, Justin A. Lemkul wrote:
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>
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Please don't post (un)subscribe requests to the list. Use
the www interface or send it to gmx-users-
requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Please don't post (un)subscribe requests to the list. Use
the www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/
users.php
--
========================================
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
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
