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

Rodrigo Faccioli 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 [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

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

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
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110927/0684e3a8/attachment.html>

More information about the gromacs.org_gmx-users mailing list