Hi,<br><br>Firstly, thanks for your help Justin.<br><br>You have already told me about the use of -ighn option. However, I've looked for an automatic way which managed the HIS protonation states. Unfortunatelly, I understood wrong about this algorithm. I believed that the difference about HSD and HSE was the names of atom.<br>
<br>Now, I use -ighn option in my algorithm. It is working fine until now.<br><br>This mess is because this structure is one of initial individuals. I'm working with an evolutionary algorithm. The final output is better. I have been trying to improve it.<br>
<br>Thanks in advance,<br><br><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>
<br><br><div class="gmail_quote">On Tue, Sep 27, 2011 at 2:10 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div><br>
<br>
Rodrigo Faccioli wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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>
</blockquote>
<br></div>
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.<div>
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Therefore I ran pdb2gmx to obtain the Hydrogen atoms is considered by Gromacs. I use the command below:<br>
<br>
/usr/local/gromacs/bin/./<u></u>pdb2gmx -f /home/faccioli/Execute/EESC_<u></u>AE/1BDD/PROT_HIS.pdb -o /home/faccioli/Execute/EESC_<u></u>AE/1BDD/prot_sys.pdb -ff charmm27 -water spc -p /home/faccioli/Execute/EESC_<u></u>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/./<u></u>pdb2gmx -f /home/faccioli/Execute/EESC_<u></u>AE/1BDD/PROT_IND_0.pdb -o /home/faccioli/Execute/EESC_<u></u>AE/1BDD/prot_sys.gro -ff charmm27 -water spc -p /home/faccioli/Execute/EESC_<u></u>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>
</blockquote>
<br></div>
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.<div>
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
All files used for my commands can be found at [3-4].<br>
<br>
[1] <a href="https://gitorious.org/protpred-gromacs/protpred-gromacs" target="_blank">https://gitorious.org/<u></u>protpred-gromacs/protpred-<u></u>gromacs</a><br>
[2] <a href="http://lists.gromacs.org/pipermail/gmx-users/2011-August/063821.html" target="_blank">http://lists.gromacs.org/<u></u>pipermail/gmx-users/2011-<u></u>August/063821.html</a><br>
[3] <a href="http://dl.dropbox.com/u/4270818/PROT_HIS.pdb" target="_blank">http://dl.dropbox.com/u/<u></u>4270818/PROT_HIS.pdb</a><br>
</blockquote>
<br></div>
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.<br>
<br>
-Justin<div><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
[4] <a href="http://dl.dropbox.com/u/4270818/prot_sys.pdb" target="_blank">http://dl.dropbox.com/u/<u></u>4270818/prot_sys.pdb</a><br>
<br>
Thanks in advance,<br>
--<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/<u></u>1025157978990218</a><br>
Public Profile - <a href="http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5" target="_blank">http://br.linkedin.com/pub/<u></u>rodrigo-faccioli/7/589/a5</a><br>
<br>
<br>
</blockquote>
<br></div>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
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