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: 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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