Hi,<br><br>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.<br><br>
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. <br>
<br>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.<br>
<br>Therefore I ran pdb2gmx to obtain the Hydrogen atoms is considered by Gromacs. I use the command below:<br><br> /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<br>
<br>In residue 19 at prot_sys.pdb there is HD1. So, HIS conformation must be HSD.<br><br>However, when I run the command below:<br><br>/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<br>
<br>shows a error message:<br>Fatal error:<br>Atom HD1 in residue HIS 19 was not found in rtp entry HSE with 17 atoms<br>while sorting atoms.<br><br>I can't understand why HSE is appeared. I appreciate any help. <br><br>
All files used for my commands can be found at [3-4].<br><br> <br>[1] <a href="https://gitorious.org/protpred-gromacs/protpred-gromacs" target="_blank">https://gitorious.org/protpred-gromacs/protpred-gromacs</a><br>[2] <a href="http://lists.gromacs.org/pipermail/gmx-users/2011-August/063821.html">http://lists.gromacs.org/pipermail/gmx-users/2011-August/063821.html</a><br>
[3] <a href="http://dl.dropbox.com/u/4270818/PROT_HIS.pdb">http://dl.dropbox.com/u/4270818/PROT_HIS.pdb</a><br>[4] <a href="http://dl.dropbox.com/u/4270818/prot_sys.pdb">http://dl.dropbox.com/u/4270818/prot_sys.pdb</a><br>
<br>Thanks in advance,<br clear="all">--<br>Rodrigo Antonio Faccioli<br>Ph.D Student in Electrical Engineering<br>University of Sao Paulo - USP<br>Engineering School of Sao Carlos - EESC<br>Department of Electrical Engineering - SEL<br>
Intelligent System in Structure Bioinformatics<br><a href="http://laips.sel.eesc.usp.br" target="_blank">http://laips.sel.eesc.usp.br</a><br>Phone: 55 (16) 3373-9366 Ext 229<br>Curriculum Lattes - <a href="http://lattes.cnpq.br/1025157978990218" target="_blank">http://lattes.cnpq.br/1025157978990218</a><br>
Public Profile - <a href="http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5" target="_blank">http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5</a><br>
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