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

Daniel Ensign densign at mail.utexas.edu
Wed Jul 14 18:06:52 CEST 2010

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

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.


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

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