[gmx-users] (no subject)

[Justin A. Lemkul]

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.

-Justin

> think that I could do? Cheers, Pyaaea
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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