Fwd: [gmx-users] Invalid atom number 6415 in indexfile

[Justin A. Lemkul]

Liu Shiyong wrote:

> 
> *.gro has no chain id information.
> I can not make energy group(based on chain id) from *.gro file generated 
> by pdb2gmx

See the mail I just sent.

> 
>  
> 
> 
>     3. Don't strip H, just to add them back again :)
> 
> 
> I have the structure minimized.pdb after EM.
> 
> minimized.pdb is output from mdrun with -c option.
> 
> I tried to feed this structure into pdb2gmx.
> I got an error.
> 
> Processing chain 1 'A' (5360 atoms, 535 residues)
> There are 803 donors and 760 acceptors
> There are 1025 hydrogen bonds
> Will use HISB for residue 212
> Will use HISB for residue 223
> Will use HISB for residue 277
> Will use HISB for residue 280
> Will use HISB for residue 374
> Will use HISB for residue 380
> Will use HISB for residue 386
> Will use HISB for residue 398
> Will use HISB for residue 425
> Will use HISB for residue 440
> 
> -------------------------------------------------------
> Program pdb2gmx, VERSION 3.3.3
> Source code file: ../../../../src/kernel/pdb2gmx.c, line: 421
> 
> Fatal error:
> Atom HD1 in residue HISB 212 not found in rtp entry with 14 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.
> -------------------------------------------------------
> 

Without -ignh, pdb2gmx expects all atoms to present and appropriately named. 
This is one of the more useful error messages, since it tells you exactly how to 
fix the problem.

-Justin

-- 
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Justin A. Lemkul
Graduate Research Assistant
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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