VMD-L Mailing List

From: Yi Shang (mirandaisbest_at_gmail.com)
Date: Wed May 20 2009 - 14:49:26 CDT

Dear there,
I wanted to load pdb files generated by VMD into tleap (in AMBER package).
But I notice that Hydrogen naming in pdb files generated by VMD, is
different from those naming of pdb files generated by tleap.
for VMD pdbs: 2HD, 3HD, 2HG, HD21, HD32.....
for tleap pdbs: HD2, HD3, HG2, 1HD2, 2HD3......

It's giving my a hard time when I use ptraj (another program in AMBER
package)
and now tleap.

I wonder how these naming inconsistency happened. And hope I can get some
suggestions here to get away with it.

Another question: the VMD pdbs are single chain molecule by default, how
could I specify it to add 'TER' in between protein, ligand, or water, water?

Thank you all! 

-- 
Miranda