[gmx-users] problem adding H atoms

Justin A. Lemkul jalemkul at vt.edu
Thu Sep 16 16:23:31 CEST 2010

Stacey Meadley wrote:
> Hi, 
> I am using pdb2gmx with amber ff and there is a problem adding the H 
> atom to the second residue of both chains  of my protein?  The residue 
> at that location is repeated in later in the chain and has no problem 
> with the hydrogens so I don't understand why it gives me the error?

Can you post some more complete information?  For example:

1. Your Gromacs version
2. Your exact command line
3. The error message you receive (copy and paste, please)
4. A snippet of your coordinate file containing the first two or three residues 
(for testing purposes)


> I relatively new to this and this is the first time I'm using amber ff 
> in gromacs so thanks for all the previous posts which help me quite a 
> bit so far.
> Stacey


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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