[gmx-users] Doubt about HSD and HSE conformation on Charmm27

[Rodrigo Faccioli]

Hi,

I have a doubt about HIS protonation state for chamm27 force field
implemented at Gromacs. I'm a computer scientist trying to understand about
protein world. So, my mistakes about protein my apologies.

I have been developing a program which reads a fasta file and builds a
protein (3D representation) based on its internal coordinates (dihedral
angles representation). This internal coordinates are based on two
libraries: CADDB 2.0 and Tuffery. The algorithm which transform internal
coordinates to cartesian coordinates (3D) is Nerf. Details about my project
you can find at [1]. I'm using Gromacs 4.5.4.

I have already started a discussion about this topic. In [2] I show Justin
answer. I understood that HSD and HSE state are based on an Gromacs
algorithm which choose HIS conformation HSD or HSE. I read pdb2gmx file and
I found set_histp function. Furthermore, I compared these conformations on
aminoacids.rtp. I seen that HSE conformation has HE2 atom instead of HD1
atom. Therefore, I understood that if the conformation contains the HD1
atom, it wiil be a HSD conformation and not HSE conformation.

Therefore I ran pdb2gmx to obtain the Hydrogen atoms is considered by
Gromacs. I use the command below:

/usr/local/gromacs/bin/./pdb2gmx -f
/home/faccioli/Execute/EESC_AE/1BDD/PROT_HIS.pdb -o
/home/faccioli/Execute/EESC_AE/1BDD/prot_sys.pdb -ff charmm27 -water spc -p
/home/faccioli/Execute/EESC_AE/1BDD/teste.top -ignh

In residue 19 at prot_sys.pdb there is HD1. So, HIS conformation must be
HSD.

However, when I run the command below:

/usr/local/gromacs/bin/./pdb2gmx -f
/home/faccioli/Execute/EESC_AE/1BDD/PROT_IND_0.pdb -o
/home/faccioli/Execute/EESC_AE/1BDD/prot_sys.gro -ff charmm27 -water spc -p
/home/faccioli/Execute/EESC_AE/1BDD/prot_sys.top

shows a error message:
Fatal error:
Atom HD1 in residue HIS 19 was not found in rtp entry HSE with 17 atoms
while sorting atoms.

I can't understand why HSE is appeared. I appreciate any help.

All files used for my commands can be found at [3-4].


[1] https://gitorious.org/protpred-gromacs/protpred-gromacs
[2] http://lists.gromacs.org/pipermail/gmx-users/2011-August/063821.html
[3] http://dl.dropbox.com/u/4270818/PROT_HIS.pdb
[4] http://dl.dropbox.com/u/4270818/prot_sys.pdb

Thanks in advance,
--
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 have a doubt about HIS protonation state for chamm27 force field
implemented at Gromacs. I'm a computer scientist trying to understand
about protein world. So, my mistakes about protein my apologies.
I have been developing a program which reads a fasta file and builds a
protein (3D representation) based on its internal coordinates (dihedral
angles representation). This internal coordinates are based on two
libraries: CADDB 2.0 and Tuffery. The algorithm which transform internal
coordinates to cartesian coordinates (3D) is Nerf. Details about my
project you can find at [1]. I'm using Gromacs 4.5.4.
I have already started a discussion about this topic. In [2] I show
Justin answer. I understood that HSD and HSE state are based on an
Gromacs algorithm which choose HIS conformation HSD or HSE. I read
pdb2gmx file and I found set_histp function. Furthermore, I compared
these conformations on aminoacids.rtp. I seen that HSE conformation has
HE2 atom instead of HD1 atom. Therefore, I understood that if the
conformation contains the HD1 atom, it wiil be a HSD conformation and
not HSE conformation.

This is incorrect. Within pdb2gmx, histidine protonation is set based on an
algorithm that searches for hydrogen bonds. The position of those hydrogen bond
acceptors dictates which form (delta protonated, HSD, or epsilon protonated,
HSE) is chosen. Neither naming nor the presence of certain H atoms can override
the algorithm.

Post by Rodrigo Faccioli
Therefore I ran pdb2gmx to obtain the Hydrogen atoms is considered by
/usr/local/gromacs/bin/./pdb2gmx -f
/home/faccioli/Execute/EESC_AE/1BDD/PROT_HIS.pdb -o
/home/faccioli/Execute/EESC_AE/1BDD/prot_sys.pdb -ff charmm27 -water spc
-p /home/faccioli/Execute/EESC_AE/1BDD/teste.top -ignh
In residue 19 at prot_sys.pdb there is HD1. So, HIS conformation must be
HSD.
/usr/local/gromacs/bin/./pdb2gmx -f
/home/faccioli/Execute/EESC_AE/1BDD/PROT_IND_0.pdb -o
/home/faccioli/Execute/EESC_AE/1BDD/prot_sys.gro -ff charmm27 -water spc
-p /home/faccioli/Execute/EESC_AE/1BDD/prot_sys.top
Atom HD1 in residue HIS 19 was not found in rtp entry HSE with 17 atoms
while sorting atoms.
I can't understand why HSE is appeared. I appreciate any help.

pdb2gmx has decided that this histidine should be epsilon protonated, and
therefore the proton at the N-delta position is extraneous. Either run pdb2gmx
with the -ignh option to remove all H atoms from the input and have them
regenerated according to what Gromacs expects, or use the -his flag to manually
choose the protonation state you want. I believe I suggested this before.

Post by Rodrigo Faccioli
All files used for my commands can be found at [3-4].
[1] https://gitorious.org/protpred-gromacs/protpred-gromacs
[2] http://lists.gromacs.org/pipermail/gmx-users/2011-August/063821.html
[3] http://dl.dropbox.com/u/4270818/PROT_HIS.pdb

I took a look at this file; its format is still incorrect and displays as a
complete mess in VMD. If you get pdb2gmx running, the output coordinate file
will be similarly mangled, or worse.

-Justin

Post by Rodrigo Faccioli
[4] http://dl.dropbox.com/u/4270818/prot_sys.pdb
Thanks in advance,
--
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

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

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

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

[Rodrigo Faccioli]

Hi,

Firstly, thanks for your help Justin.

You have already told me about the use of -ighn option. However, I've looked
for an automatic way which managed the HIS protonation states.
Unfortunatelly, I understood wrong about this algorithm. I believed that the
difference about HSD and HSE was the names of atom.

Now, I use -ighn option in my algorithm. It is working fine until now.

This mess is because this structure is one of initial individuals. I'm
working with an evolutionary algorithm. The final output is better. I have
been trying to improve it.

Thanks in advance,


--
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

Post by Justin A. Lemkul

Post by Rodrigo Faccioli
Hi,
I have a doubt about HIS protonation state for chamm27 force field
implemented at Gromacs. I'm a computer scientist trying to understand about
protein world. So, my mistakes about protein my apologies.
I have been developing a program which reads a fasta file and builds a
protein (3D representation) based on its internal coordinates (dihedral
angles representation). This internal coordinates are based on two
libraries: CADDB 2.0 and Tuffery. The algorithm which transform internal
coordinates to cartesian coordinates (3D) is Nerf. Details about my project
you can find at [1]. I'm using Gromacs 4.5.4.
I have already started a discussion about this topic. In [2] I show Justin
answer. I understood that HSD and HSE state are based on an Gromacs
algorithm which choose HIS conformation HSD or HSE. I read pdb2gmx file and
I found set_histp function. Furthermore, I compared these conformations on
aminoacids.rtp. I seen that HSE conformation has HE2 atom instead of HD1
atom. Therefore, I understood that if the conformation contains the HD1
atom, it wiil be a HSD conformation and not HSE conformation.

This is incorrect. Within pdb2gmx, histidine protonation is set based on
an algorithm that searches for hydrogen bonds. The position of those
hydrogen bond acceptors dictates which form (delta protonated, HSD, or
epsilon protonated, HSE) is chosen. Neither naming nor the presence of
certain H atoms can override the algorithm.
Therefore I ran pdb2gmx to obtain the Hydrogen atoms is considered by

Post by Rodrigo Faccioli
/usr/local/gromacs/bin/./**pdb2gmx -f /home/faccioli/Execute/EESC_**AE/1BDD/PROT_HIS.pdb
-o /home/faccioli/Execute/EESC_**AE/1BDD/prot_sys.pdb -ff charmm27 -water
spc -p /home/faccioli/Execute/EESC_**AE/1BDD/teste.top -ignh
In residue 19 at prot_sys.pdb there is HD1. So, HIS conformation must be
HSD.
/usr/local/gromacs/bin/./**pdb2gmx -f /home/faccioli/Execute/EESC_**AE/1BDD/PROT_IND_0.pdb
-o /home/faccioli/Execute/EESC_**AE/1BDD/prot_sys.gro -ff charmm27 -water
spc -p /home/faccioli/Execute/EESC_**AE/1BDD/prot_sys.top
Atom HD1 in residue HIS 19 was not found in rtp entry HSE with 17 atoms
while sorting atoms.
I can't understand why HSE is appeared. I appreciate any help.

pdb2gmx has decided that this histidine should be epsilon protonated, and
therefore the proton at the N-delta position is extraneous. Either run
pdb2gmx with the -ignh option to remove all H atoms from the input and have
them regenerated according to what Gromacs expects, or use the -his flag to
manually choose the protonation state you want. I believe I suggested this
before.
All files used for my commands can be found at [3-4].

Post by Rodrigo Faccioli
[1] https://gitorious.org/**protpred-gromacs/protpred-**gromacs<https://gitorious.org/protpred-gromacs/protpred-gromacs>
[2] http://lists.gromacs.org/**pipermail/gmx-users/2011-**
August/063821.html<http://lists.gromacs.org/pipermail/gmx-users/2011-August/063821.html>
[3] http://dl.dropbox.com/u/**4270818/PROT_HIS.pdb<http://dl.dropbox.com/u/4270818/PROT_HIS.pdb>

I took a look at this file; its format is still incorrect and displays as a
complete mess in VMD. If you get pdb2gmx running, the output coordinate
file will be similarly mangled, or worse.
-Justin
[4] http://dl.dropbox.com/u/**4270818/prot_sys.pdb<http://dl.dropbox.com/u/4270818/prot_sys.pdb>

Post by Rodrigo Faccioli
Thanks in advance,
--
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<http://lattes.cnpq.br/1025157978990218>
Public Profile - http://br.linkedin.com/pub/**rodrigo-faccioli/7/589/a5<http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5>

--
==============================**==========
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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================**==========
--
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