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:
http://folding.stanford.edu/ffamber/
Tom
--On 30 May 2007 13:05 -0700 bo yang [EMAIL PROTECTED] 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
[EMAIL PROTECTED]
University of Bristol, UK.
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