Re: Residue number changed to hexadecimal string

From: Jim Phillips (
Date: Fri Feb 06 2015 - 00:38:00 CST

Are you sure that's not an insertion code? In any case, you would need to
determine which code modified your residue numbers at what step (i.e., is
there a residue 297a in the psf file and what tool wrote the psf file).


On Fri, 6 Feb 2015, K Miura wrote:

> Dear NAMD users,
> I encountered an problem that residue numbers of .pdb file become
> hexadecimal string.
> I performed MD of a channel protein and its ligand.
> The protein consists of 4 identical subunits, each of them contain 501
> amino acids.
> The ligand is 2-APB ( 2-Aminoethoxydiphenyl borate, C14H16BNO).
> I added POPC membrane bilayer and water molecules. The structure data
> consists of about 115,000 atoms.
> Then the structure was subjected to MM calculation by MOE (Molecular
> Operating Environment), followed by
> 5000ps of MD simulation by NAMD version 2.8.
> After the MD simulation, I opened .psf and .coor.dcd files by VMD
> version 1.9 and saved the last snapshot as .pdb file.
> When I opened the .pdb file, I found residue numbers were changed to
> hexadecimal string ("297a" for example).
> The input data (PDB file) had no problem (decimal number for residue
> numbers).
> MD simulation without the ligand didn't have the same problem.
> Has anyone had similar problem?
> If so, how can I avoid this problem?
> Best regards
> Kenji Miura
> Kobe University Graduate school of Medicine

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