[gmx-users] HIS N Terminal - Charmm27 force field

[Rodrigo Faccioli]

Hi,

I would like to know what configuration is used for HIS when it is N
Terminal. I use charmm27 force-field. I've read at aminoacids.rtp file that
HIS has HSD, HSP and HSE entries. I understood HSE is used when HIS is
internal residue (it is neither N nor C terminal residue) and HSD is used
when HIS is N terminal. The last entry (HSD) has HD1 atom. HSE has HE1 atom
instead of HD1.

However, when I run pdb2gmx I receive an error message:
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.4
Source code file: /home/faccioli/gromacs-4.5.4/src/kernel/pdb2gmx.c, line:
655

Fatal error:
Atom HD1 in residue HIS 1 was not found in rtp entry HSE with 19 atoms
while sorting atoms.

For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Anyway, I ran HIS N terminal as HSE entry. I received an error message:

Program pdb2gmx, VERSION 4.5.4
Source code file: /home/faccioli/gromacs-4.5.4/src/kernel/pdb2gmx.c, line:
655

Fatal error:
Atom HE2 in residue HIS 1 was not found in rtp entry HSD with 19 atoms
while sorting atoms.

Read more details about pdb2gmx out, I found:
Will use HISD for residue 1
Will use HISE for residue 3

Below I show my pdb files which I used. In [1] shows the pdb file I used to
run HIS N Terminal considering HSD entry. So I used HD1 atom. In [2] shows
the pdb file I used to run HIS N Terminal considering HSE entry. So I used
HE2 atom.

[1] http://dl.dropbox.com/u/4270818/PROT_HSD.pdb
[2] http://dl.dropbox.com/u/4270818/PROT_HSE.pdb

I appreciate any help.

Thanks,

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: [phone] Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
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[Justin A. Lemkul]

Post by Rodrigo Faccioli
Hi,
I would like to know what configuration is used for HIS when it is N
Terminal. I use charmm27 force-field. I've read at aminoacids.rtp file
that HIS has HSD, HSP and HSE entries. I understood HSE is used when HIS
is internal residue (it is neither N nor C terminal residue) and HSD is
used when HIS is N terminal. The last entry (HSD) has HD1 atom. HSE has
HE1 atom instead of HD1.

HSD vs. HSE has nothing to do with whether the histidine is terminal or
internal. Epsilon and delta protonation are determined by an algorithm that
predicts which N should have the H atom based on local hydrogen bonding. In
principal, HSD and HSE can occur anywhere in the protein chain.

Post by Rodrigo Faccioli
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.4
Source code file: /home/faccioli/gromacs-4.5.4/src/kernel/pdb2gmx.c,
line: 655
Atom HD1 in residue HIS 1 was not found in rtp entry HSE with 19 atoms
while sorting atoms.
For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.4
Source code file: /home/faccioli/gromacs-4.5.4/src/kernel/pdb2gmx.c,
line: 655
Atom HE2 in residue HIS 1 was not found in rtp entry HSD with 19 atoms
while sorting atoms.
Will use HISD for residue 1
Will use HISE for residue 3
Below I show my pdb files which I used. In [1] shows the pdb file I used
to run HIS N Terminal considering HSD entry. So I used HD1 atom. In [2]
shows the pdb file I used to run HIS N Terminal considering HSE entry.
So I used HE2 atom.
[1] http://dl.dropbox.com/u/4270818/PROT_HSD.pdb
[2] http://dl.dropbox.com/u/4270818/PROT_HSE.pdb
I appreciate any help.

All of this boils down to naming mismatches, as the original error indicates.
Your naming does not conform to the expected contents of any histidine .rtp
entry. Name your atoms appropriately, or use -ignh to have pdb2gmx rebuild what
it thinks should be there (which can also be tweaked with the -his flag if you
are unhappy with the chosen protonation state). Also note that your .pdb files
do not conform to PDB standard, so pdb2gmx may not interpret the coordinates
correctly. The files display as a complete jumble, indicating spacing issues.

-Justin
--
========================================

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

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