Hi MD community:
I encountered some problems while generating psf file. As we know, PDB only assumes atom names containing up to 4 characters. However, if the atom name in CHARMM topology is more than 4 characters, how do we manage our pdb file?
Hello! if you want to build the PSF/PDB files in VMD (ie., using psfgen), you can use the command "pdbalias".
Let's see one example, if you want to simulate one cardiolipin molecule (an important lipid in the inner mitochondrial membrane), which has the resname TLCL2 in the charmm force field (see the official release at toppar/stream/lipid/toppar_all36_lipid_cardiolipin.str), but your initial PDB file has a resname of this molecule with a maximum of four characters, ie., TLCL for this example. Here, you will add the following line in your psfgen script.
pdbalias residue TLCL TLCL2
Thus, when psfgen reads the pdb with the resname TLCL, it will search in the charmm topology file (*.rtf file) the molecule with the resname TLCL2 (instead TLCL).
Best regards!
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