Hi, 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.
However, when I run pdb2gmx I receive an error message: ------------------------------------------------------- Program pdb2gmx, VERSION 4.5.4 Source code file: /home/faccioli/gromacs-4.5.4/src/kernel/pdb2gmx.c, line: 655 Fatal error: Atom HD1 in residue HIS 1 was not found in rtp entry HSE with 19 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 & H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- Anyway, I ran HIS N terminal as HSE entry. I received an error message: Program pdb2gmx, VERSION 4.5.4 Source code file: /home/faccioli/gromacs-4.5.4/src/kernel/pdb2gmx.c, line: 655 Fatal error: Atom HE2 in residue HIS 1 was not found in rtp entry HSD with 19 atoms while sorting atoms. Read more details about pdb2gmx out, I found: Will use HISD for residue 1 Will use HISE for residue 3 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. [1] http://dl.dropbox.com/u/4270818/PROT_HSD.pdb [2] http://dl.dropbox.com/u/4270818/PROT_HSE.pdb I appreciate any help. Thanks, -- 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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