[AMBER] topology problems

From: Seibold, Steve Allan <stevesei.ku.edu>
Date: Tue, 7 Apr 2020 16:58:59 +0000

I have added a protein subunit (called A) to another protein(B) and created one polypeptide chain AB. There are no "TER" commands and the system is recognized and the prmtop and inpcrd files are built using tleap with no problem. The output pdb files (using leap) are fine-one polypeptide chain AB. When I use the output file prmtop to produce a pdb file of the inpcrd file, again there is no problem. It's a AB polypeptide.

However, when I do an energy minimization and convert file.rst to a file.pdb using "ambpdb -p prmtop -c file.rst > file.pdb", the resulting pdb file separates the subunit A from B by creating an "OXT" at the end of A. That is A-oxt and thus becomes a separate subunit. Since the prmtop file does not call for a OXT at that position, how is ambpdb creating it?

I am visualizing using VMD. I even loaded first the prmtop file and then the pdb file (of the restart file) and got A-oxt..

Thanks, Steve
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Received on Tue Apr 07 2020 - 10:00:02 PDT
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