[gmx-users] (no subject)

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 30 19:35:31 CEST 2009

Asmaa Elsheshiny wrote:
> Hi, everybody, I tried to use pdb2gmx program to obtain .top& .gro files  but
> I eceived the following error message Fatal error: Atom HB3 in residue ARG 1
> not found in rtp entry with 24 atoms while sorting atoms. Maybe different
> protonation state. Remove this hydrogen or choose a different protonation
> state. Option -ignh will ignore all hydrogens in the input. even when i add a
> n&c termials to the peptide, I find that there is no difference in the error
> message also I checked .rtp file and if find there is no HB3 ( there is no 3
> in any of the atomic numbering in any of the aminoacids residues), so I
> modified the .pdb file by changing thr numbering. But this affects
> dramatically the shape of the the molecule ( cause distruction of certain

Probably because you altered the spacing of the .pdb file when you made changes.

> portions of it). I do not want to use the flag -ignh because when i made this
> the molecule has changed greatly and affects my results badly. So what do you

Don't know what you mean here.  Using -ignh is the best solution.  If that H is 
necessary under your given force field, it will be added back and given the 
proper name.


> think that I could do? Cheers, Pyaaea
> _______________________________________________ gmx-users mailing list
> gmx-users at gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 
> Please search the archive at http://www.gromacs.org/search before posting! 
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org. Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list