I am doing MD simulation for Gla domain of factor IX (45aa) using gromacs and gromos force field. Gla domain contains 12 gamma carboxy glutamic acids and 12 Ca2+ ions. The input pdb file for gromacs has 2 chain (chain A for amino acid sequence and chain B for Ca2+). But the out put file after MD has only one chain containing amino acid sequence and ions. I don't know why?
What command option did you use during pdb2gmx?
you used -renum option? How many .itp file generated ?
You should do simply like
pdb2gmx -f xxxx.pdb -o xxxxx.gro (pdb)
it will generate 2 itp topology files for protein and ions aswell as protein with chainsA, B.
What is the "output" file? If you mean the .gro file generated automatically after the MD simulation, then there's probably no chain information included, only the coordinates. You can generate the 'end' structure file by using trjconv, with the .tpr file and the .gro file. They should be in different chains, as long as the .top file is correct.
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