VMD-L Mailing List

From: YangMingjun (mjyang_at_dicp.ac.cn)
Date: Tue Mar 02 2010 - 10:50:13 CST

Dear all,
   I am going to create a psf file for the protein-RNA complex by psfgen. But output message manifested something wrong.
The input file I used is:
---- psf.tcl
# (1) Split input PDB file into segments}
# (2) Embed the psfgen commands in this script
psfgen << ENDMOL
# (3) Read topology file
topology top_all27_prot_na.rtf
# (A) Build protein segment
segment A {
 pdb protein-min-a.pdb
}
# (A) Read protein coordinates from PDB file
coordpdb protein-min-a.pdb A
############################
# (A) Build protein segment
segment B {
 pdb rna-min-b.pdb
}
# (A) Read protein coordinates from PDB file
coordpdb rna-min-b.pdb B

writepsf system.psf
writepdb system.pdb
# End of psfgen commands
ENDMOL
---------

Part of the output is:
-------
...
building segment B
reading residues from pdb file rna-min-b.pdb
extracted 47 residues from pdb file
Info: generating structure...
Info: skipping conformation O3'-O5'-P-O2P at beginning of segment.
Info: skipping conformation O3'-O5'-P-O1P at beginning of segment.
Info: skipping conformation O3'-P-O5'-C5' at beginning of segment.
Info: skipping bond O3'-P at end of segment.
Info: skipping conformation C3'-O3'-P-O5' at end of segment.
Info: skipping conformation C4'-C3'-O3'-P at end of segment.
no atom C in residue GUA:1 of segment B
Warning: add conformation failed in patch NTER
B:1
no atom CA in residue CYT:47 of segment B
Warning: add improper failed in patch CTER
no atom CA in residue CYT:47 of segment B
Warning: add conformation failed in patch CTER
no atom N in residue CYT:47 of segment B
Warning: add conformation failed in patch CTER
B:47
Info: segment complete.
reading coordinates from pdb file rna-min-b.pdb for segment B
Warning: failed to set coordinate for atom H5T GUA:1 B
Warning: failed to set coordinate for atom H3T CYT:47 B
Info: writing psf file system.psf
...
------

It seems that there is something wrong with the 3' and 5' terminal ends of the RNA segment.
Could someone please tell me how to fix this problem?

Another question is where to find the manual for psfgen?

Thanks for the time.
 

Yang Mingjun

2010-03-03

-----------------------------------------------
  State Key Lab of Molecular Reaction Dynamics (SKLMRD),
  Dalian Institute of Chemical Physics(DICP),
  the Chinese Academy of Sciences(CAS),
  
  Zhongshan Road457, Dalian City,
  Liaoning Province 116023,P. R. China