[gmx-users] residue names for AMBER ff in GROMACS

Sun Mar 30 16:51:41 CEST 2008

Hi all,

I had a problem of converting of definition of residue names of AMBER96 ff in GROMACS package. 

Although I changed the residue names acc. to those defined in AMBER96 ff in my PDB file, I had the following error: (I have searched the mailing archieves for this error.)

WARNING: atom H is missing in residue GLN 1 in the pdb fileYou might need to add atom H to the hydrogen database of   
residue GLN in the file ff???.hdb (see the manual).

I looked at both .rtp and hdb files in order to investigate whether there are missing residues in these files, but  the GLN residue name and the corresponding H names of this residue have been defined in .rtp and .hdb,respectively.

So, what may be  the problem?

Thanks in advance

Ozge Engin
Computational Science & Engineering
Koc University

More information about the gromacs.org_gmx-users mailing list