[gmx-users] version 4 pdb2gmx with ffamber broken on Mac?

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 14 18:36:12 CEST 2010

Daniel Ensign wrote:
> While trying to get the gro and topology on a Mac using GMX v. 4.0.5 or
> 4.0.7, I get from running pdb2gmx -f myfile.pdb -ff amber03 -ignh
> WARNING: atom H is missing in residue ALA 2 in the pdb file
>          You might need to add atom H to the hydrogen database of
>          residue ALA in the file ff???.hdb (see the manual)
> This effect appears even after tricks like deleting ALA 2, putting an H
> atom in manually, among other things.
> Things that work:
> 1. Same command works on Linux using GMX 4.0.5
> 2. Same command works on Mac using GMX 3.3.1
> 3. Same command works if I use OPLS/AA-L rather than ffamber03
> To reiterate, things that don't work:
> 1. Command gives the above WARNING on Mac using GMX 4.0.5 and 4.0.7
> 2. Command gives the above WARNING on Mac using GMX 4.0.5 using
> ffamber99sb
> I did not test any other platforms or force fields.
> Please let me know if contacting the Master and Commander of ffamber
> directly rather than bothering you folks.

Are you using the correct nomenclature for the terminal residues?  I know I've 
seen this happen if the first residue is not appropriately named NXXX.  Point #2 



> Thanks,
> Dan


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


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