Hi all gmxers, I'm trying to analyze an amber dynamic (v.8) with the gromacs tools (last version). Sorry in advance for the long message. To do so, I'm trying to generate also a tpr file (needed by some tools). My procedure is being to convert all the MD in multiple pdb format. So I have extracted the first frame to generate a .top file. So I've converted the pdb res atom names that didn't match the OPLS-All atom FF (6th option): sed -e "/ATOM/s/HIE/HIS/g" -e "/ATOM/s/NME/NAC/g" -e "/ATOM/s/HB3 GLU/HB1 GLU/g" -e "/ATOM/s/HG3 GLU/HG1 GLU/g" -e "/ATOM/s/HB3 LEU/HB1 LEU/g" -e "/ATOM/s/HB3 ASP/HB1 ASP/g" -e "/ATOM/s/HG3/HG1/g" -e "/ATOM/s/HG13 ILE/HG11 ILE/g" -e "/ATOM/s/HD3 LYS/HD1 LYS/g" -e "/ATOM/s/HE3 LYS/HE1 LYS/g" -e "/ATOM/s/HD3 ARG/HD1 ARG/g" -e "/ATOM/s/HD3 PRO/HD1 PRO/g" -e "/ATOM/s/HA3 GLY/HA1 GLY/g" pdb_orig.pdb > pdb_ok.pdb This made pdb2gmx work without problems generating .top and .gro files...so with these files i will generate a tpr file. Now the problem is that the atom order is different between the gro file and the multiple pdb file (the original trajectory). Is there a way to make the trajectory (original) in the correct order (that comes from the gromacs new files)? If yes, please tell me a solution in a step-by-step way. Many thanks to all Andrea
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