[gmx-users] Regarding Atom in residue XXX was not found in rtp entry with xxx atoms while sorting atoms

Mark Abraham mark.j.abraham at gmail.com
Thu Aug 24 16:47:13 CEST 2017


pdb2gmx is giving you the normal termini found in a peptide in aqueous
solution near physiological pH, ie. zwitterionic. You can choose different
termini if your force field supports it, but you should only do so if you
are modelling something that requires a non-zwitterionic form.


On Thu, Aug 24, 2017 at 3:48 PM Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:

> Hello,
> I have a amino acid and i am using charmm 36 FF to create the topology by:-
>  gmx pdb2gmx -f abc.pdb -o abc.gro....but i am getting error as:-
> Atom HO in residue XXX was not found in rtp entry with xxx atoms while
> sorting atoms.
> So  if i use the -ignh flag in the gmx pdb2gmx command, i am getting the
> topology and the .gro file, but i  in the .gro file the  the hydrogen in
> the OH ie., in C terminal, is getting attached to N terminal (which was NH2
> initially but in the .gro file it getting converted into NH3). So how do i
> avoid the hydrogen getting shifted from OH or C terminal side to N terminal
> side..??
> How can i solve this error..??
> Thank you...
> --
> With Best Regards,
> Ph.D Student
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