A strange thing about psfgen~

From: κ (weikai_at_ustc.edu)
Date: Sat Nov 13 2004 - 06:21:35 CST

hi,every I found a strange question about the psf generation.
The phenomenas are below:
Q1.When I use the top_all27_prot_na.rtf topology file that contains protein and na topology information,the psfgen outpu :
Created by CHARMM version 31 1
ERROR! FAILED TO RECOGNIZE CMAP
ERROR! FAILED TO RECOGNIZE CMAP.Why?
Q2.I have download a pdb file for protein data bank and the file contain 128 water molecules,but when I use psfgen it can recognize the 3waters of the beginning ,but from 4 to end it indicate:
  "reading residues from pdb file pre.pdb
   duplicate residue key 4
   ERROR: failed on residue HOH from pdb file
   ...........
  "
just the 3 water of the beginning is ok,I don't know why?
Q3.at the last it indicates that:
Warning: failed to guess coordinates for 13 atoms
Can anyone tell me how to resolve these problems,thank you very much.
 
                                                  respectfully,Kai

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