[gmx-users] Doubt about HSD and HSE conformation on Charmm27
rodrigo_faccioli at uol.com.br
Tue Sep 27 18:41:05 CEST 2011
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 . I'm using Gromacs 4.5.4.
I have already started a discussion about this topic. In  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:
/home/faccioli/Execute/EESC_AE/1BDD/prot_sys.pdb -ff charmm27 -water spc -p
In residue 19 at prot_sys.pdb there is HD1. So, HIS conformation must be
However, when I run the command below:
/home/faccioli/Execute/EESC_AE/1BDD/prot_sys.gro -ff charmm27 -water spc -p
shows a error message:
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].
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
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
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