From: K Miura (080m812m_at_stu.kobe-u.ac.jp)
Date: Thu Feb 05 2015 - 23:34:24 CST
Dear NAMD users,
I encountered an problem that residue numbers of .pdb file become
I performed MD of a channel protein and its ligand.
The protein consists of 4 identical subunits, each of them contain 501
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
MD simulation without the ligand didn't have the same problem.
Has anyone had similar problem?
If so, how can I avoid this problem?
Kobe University Graduate school of Medicine
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