[gmx-users] genion command with PDB files for amber03 force field

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Mar 9 23:04:42 CET 2009


To set things straight a bit.

>> "If you are using ion-related GROMACS tools, such as genion, you will need
>> to enter the AMBER ion definition to the ions.itp file in the "top"
>> directory of the GROMACS distribution."
> This isn't too tough, as all the parameters for the ions are included with
> the Amber ports, but genion needs them to be in the ions.itp (or other
> suitable) file.

This has nothing to do with genion. Genion just uses the names for
ions that are given (either explicitly or as default) with options
-pname and -nname. When the ions occur in the system (under [ system ]
in the .top file), they have to be defined somewhere as moleculetypes.
Otherwise grompp will complain; no other program. ions.itp is just an
intuitive place for these moleculetype definitions. Please inform
yourself well regarding the way gromacs handles topologies. Check
chapter 5 of the manual. This goes double when answering posts on such
topics. Although such efforts are commonly appreciated, (partly) wrong
information may send the original poster further off.

>> Dear gromacs users,
>> I am using genion command to add ions to .tpr file which
>> was made for protein by use of amber03 force field.
>> In intial pdb file N-terminal amino acid is NHIE, but genion changes it to
>> NHI, which isnot recognized by next pdb2gmx.
>> This is not a big problem , but it looks is a little bit like a bug.

Justin answered this part of the question. For a suitable scheme to
set up your simulations, you may want to check



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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