[gmx-users] C-terminal amidation of peptide

[anna Kalkbrenner]

Hello,

I'm sorry if my questions are on the elementary level, as I am still
learning how to use GROMACS. I would like perform an MD run on a peptide
that has an amidated c-terminal. My understanding is that I can modify my
PDB structure to include the NH2 group. Then, with pdb2gmx I use the "-ter"
option and select "none" for the C-terminus. Is this correct? What is the
best way to edit the PDB file to add the amide group? Can it be done
through a structural editor?

Best regards,

Anna
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[Justin A. Lemkul]

Post by anna Kalkbrenner
Hello,
I'm sorry if my questions are on the elementary level, as I am still
learning how to use GROMACS. I would like perform an MD run on a
peptide that has an amidated c-terminal. My understanding is that I can
modify my PDB structure to include the NH2 group. Then, with pdb2gmx I
use the "-ter" option and select "none" for the C-terminus. Is this
correct? What is the best way to edit the PDB file to add the amide
group? Can it be done through a structural editor?

Your approach is correct. Use your favorite editing software to add the
appropriate group. There are some useful programs listed on the Gromacs site,
but unfortunately it is currently down. xLeap is a pretty useful tool, although
there are many others that can accomplish the same; for simple amide addition
you could probably add it manually with a bit of geometry :)

-Justin

Post by anna Kalkbrenner
Best regards,
Anna

--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | [phone]
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================

[Mark Abraham]

Post by anna Kalkbrenner
Hello,
I'm sorry if my questions are on the elementary level, as I am still learning how to use GROMACS.? I would like perform an MD run on a peptide that has an amidated c-terminal.? My understanding is that I can modify my PDB structure to include the NH2 group.? Then, with pdb2gmx I use the "-ter" option and select "none" for the C-terminus.? Is this correct?

Correct treatment of termini differs widely with the forcefield. Some forcefields have special residue types that contain just the terminal atoms, some force fields have special residue types and include the whole residue preceding the terminal atoms and the terminal atoms. You will need to look in the residuetypes.rtp file for the forcefield you have in mind and see what possibilities are already supported.

pdb2gmx -ter and "none" merely directs pdb2gmx not to change anything using the terminus databases (.tdb), however what is in your input coordinate file (and now unmodified) still has to be supported by the .rtp. More details in chapter 5 of the manual, of course.

Post by anna Kalkbrenner
? What is the best way to edit the PDB file to add the amide group?? Can it be done through a structural editor?

Yes.

Mark
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[Jianguo Li]

If you use CHARMM FF and Gromacs4.5 or later, you can use -ter in pdb2gmx and
choose CT2 to add NH2 at C-terminus. For other FF, you may need to manually add
NH2 in pdb file.

Jianguo





________________________________
From: anna Kalkbrenner <anna.kalkbrenner at gmail.com>
To: gmx-users at gromacs.org
Sent: Sunday, 20 March 2011 11:59:34
Subject: [gmx-users] C-terminal amidation of peptide

Hello,

I'm sorry if my questions are on the elementary level, as I am still learning
how to use GROMACS. I would like perform an MD run on a peptide that has an
amidated c-terminal. My understanding is that I can modify my PDB structure to
include the NH2 group. Then, with pdb2gmx I use the "-ter" option and select
"none" for the C-terminus. Is this correct? What is the best way to edit the
PDB file to add the amide group? Can it be done through a structural editor?

Best regards,

Anna


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