[gmx-users] Question about MD simulation

TJ Piggot t.piggot at bristol.ac.uk
Thu May 31 00:33:58 CEST 2007

You want to name the atoms according to the atom types in ffamberXX.rtp 
file. For an example of this for DNA see the dickerson.pdb provided in the 
README directory of the ffamber port or this pdb can be downloaded on its 
own from:



--On 30 May 2007 13:05 -0700 bo yang <suriayang at gmail.com> wrote:

> Dear gromacs users,
> I have a quetion regarding using amber forcefield in gromacs.
> I did the DNA and water interaction simulation. After the energy
> minimization, the
> original helix-structured DNA becomes two fragments. At this stage,
> I assume that the "simulation process" is correct.
> I used exactly same energy minimization em.mdp file for my nanotube-water
> simulation. Since I am using amber forcefield, I changed the name of all
> atoms (C, H) of my nanotube according to the name used in ffamberXX.itp.
> For example, C is renamed as amberXX_42.
> During the energy minimization, I got warning messages as:
> WARNING: Writing out atom name (amber) longer than 4 characters to .pdb
> file
> Also, the EM result is "Segmentation Fault".
> Can anyone give me some suggstions or hints how to solve the problem?
> Is there any other ways to rename those atoms (either in NT or amber
> files)?
> Thank you very much!
> Bo

TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.

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