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