[gmx-users] PDB2GMX Fatal Error

Reza Esmaeili goldeagle.93 at gmail.com
Wed Mar 1 07:54:49 CET 2017


Use -ignh in pdb2gmx.

> On Mar 1, 2017, at 10:22, Syed Azeem <syedazeemullah186 at gmail.com> wrote:
> 
> Hi all,
> 
> I tried passing a predicted peptide (16-mer) into GMX and ended up
> with a fatal error regarding hydrogen. I tried ignoring the hydrogens
> using -ignh command. But I'll need to calculate H-bonds for the next
> analysis, as I'll dock this peptide into a target protein.
> 
> Fatal error:
> Atom HB3 in residue ASN 1 was not found in rtp entry NASN with 16 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.
> 
> How to solve this issue?
> 
> Thanks in advance
> 
> Azeem
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.



More information about the gromacs.org_gmx-users mailing list