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

[Daniel Ensign]

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.

Thanks,
Dan

-- 
Tu ne cede malis, sed contra audentior ito. -- Virgil