[gmx-users] HIS N Terminal - Charmm27 force field

[Rodrigo Faccioli]

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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