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

[Justin A. Lemkul]

Rodrigo Faccioli wrote:
> 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.
> 

HSD vs. HSE has nothing to do with whether the histidine is terminal or 
internal.  Epsilon and delta protonation are determined by an algorithm that 
predicts which N should have the H atom based on local hydrogen bonding.  In 
principal, HSD and HSE can occur anywhere in the protein chain.

> 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.
> 

All of this boils down to naming mismatches, as the original error indicates. 
Your naming does not conform to the expected contents of any histidine .rtp 
entry.  Name your atoms appropriately, or use -ignh to have pdb2gmx rebuild what 
it thinks should be there (which can also be tweaked with the -his flag if you 
are unhappy with the chosen protonation state).  Also note that your .pdb files 
do not conform to PDB standard, so pdb2gmx may not interpret the coordinates 
correctly.  The files display as a complete jumble, indicating spacing issues.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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