[gmx-users] Reordering problem AMBER to GROMACS

andrea carotti andcar at chimfarm.unipg.it
Tue Oct 17 17:22:56 CEST 2006

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 

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