Hi,<br><br>I would like to know what configuration is used for HIS when it is N Terminal. I use charmm27 force-field. I've read at aminoacids.rtp file that HIS has HSD, HSP and HSE entries. I understood HSE is used when HIS is internal residue (it is neither N nor C terminal residue) and HSD is used when HIS is N terminal. The last entry (HSD) has HD1 atom. HSE has HE1 atom instead of HD1.<br>
<br>However, when I run pdb2gmx I receive an error message: <br>-------------------------------------------------------<br>Program pdb2gmx, VERSION 4.5.4<br>Source code file: /home/faccioli/gromacs-4.5.4/src/kernel/pdb2gmx.c, line: 655<br>
<br>Fatal error:<br>Atom HD1 in residue HIS 1 was not found in rtp entry HSE with 19 atoms<br>while sorting atoms.<br><br>For a hydrogen, this can be a different protonation state, or it<br>might have had a different number in the PDB file and was rebuilt<br>
(it might for instance have been H3, and we only expected H1 & H2).<br>Note that hydrogens might have been added to the entry for the N-terminus.<br>Remove this hydrogen or choose a different protonation state to solve it.<br>
Option -ignh will ignore all hydrogens in the input.<br>For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br><br>Anyway, I ran HIS N terminal as HSE entry. I received an error message:<br><br>Program pdb2gmx, VERSION 4.5.4<br>Source code file: /home/faccioli/gromacs-4.5.4/src/kernel/pdb2gmx.c, line: 655<br>
<br>Fatal error:<br>Atom HE2 in residue HIS 1 was not found in rtp entry HSD with 19 atoms<br>while sorting atoms.<br><br>Read more details about pdb2gmx out, I found:<br>Will use HISD for residue 1<br>Will use HISE for residue 3<br>
<br>Below I show my pdb files which I used. In [1] shows the pdb file I used to run HIS N Terminal considering HSD entry. So I used HD1 atom. In [2] shows the pdb file I used to run HIS N Terminal considering HSE entry. So I used HE2 atom.<br>
<br>[1] <a href="http://dl.dropbox.com/u/4270818/PROT_HSD.pdb">http://dl.dropbox.com/u/4270818/PROT_HSD.pdb</a><br>[2] <a href="http://dl.dropbox.com/u/4270818/PROT_HSE.pdb">http://dl.dropbox.com/u/4270818/PROT_HSE.pdb</a><br>
<br>I appreciate any help. <br><br>Thanks,<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>
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