[gmx-users] Error in MD

Mark Abraham Mark.Abraham at anu.edu.au
Wed Dec 14 14:12:26 CET 2005

Dhananjay joshi wrote:
> 1. pdb2gmx -f CORE_MTB.pdb -o CORE_MTB.gro -p CORE_MTB.top
> It has generated fatal error as follows
> Fatal error:
> Atom HD1 in residue HISB 61 not found in rtp entry with 12 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.
> Then I used -ignh option and the steps are as follows..

That might be a reasonable thing to do, depending on your system. Have a 
look at the resulting .gro file using something that can read it (e.g. 
VMD) and verify that it looks protein-like. That might be a complex 
process if you have a complex system, but it's time well spent.

In general, warning & error messages are not there because the 
programmer is too stupid to make it work without giving such messages. 
They are usually there either because the user has done something 
incorrect, or (in the case of gromacs) because there's a relevant 
question, about which the user needs to make a (scientific) judgement, 
that it would be inappropriate for gromacs to blithely gloss over. The 
latter is true here, and generally so for histidine residues.

> 2. editconf -f CORE_MTB.gro -o CORE_MTB.gro -d 0.8
> WARNING: No boxtype specified - distance condition applied in each dimension.
> If the molecule rotates the actual distance will be smaller. You might want
> to use a cubic box instead, or why not try a dodecahedron today?

Unless you can say why you want a triclinic box (the default), while 
you're learning I strongly recommend a cubic box... use the -b option 

> 3. genbox -cp CORE_MTB.gro -cs -o CORE_MTB_b4em.gro -p CORE_MTB.top

Have a look at the resulting structure and check for broken or 
inappropriately placed water molecules.

> The mdp file used for grompp amd mdrun is as follows..

It looked sensible for EM.


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