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

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 27 19:10:19 CEST 2011

Rodrigo Faccioli wrote:
> 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 
> 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.

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].
> [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.


> [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: 55 (16) 3373-9366 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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