RE: Unusual bond between residues: 0 (none) and 1 (protein)

From: Song, Hyundeok (songhk) (songhk_at_mail.uc.edu)
Date: Fri Oct 16 2009 - 22:23:29 CDT

Dear NAMD users

I tried to fix this problem in various ways, but I couldn't.
Instead I checked same pdb file(combined protein with lipid) at another visual program, which showed the bond connection between residue 0 and 1.

** my thought **
Visually I can't see the bond connection between residue 0 and 1 at vmd, but that doesn't mean disconnection between residues.
There is a bond connection even though I can't see the bond connection.
Formy(resid 0) moves near VAL(resid 1) during simulation. It didn't run away.
I think I don't need worry about this.

 Hyun.

________________________________________
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of Song, Hyundeok (songhk) [songhk_at_mail.uc.edu]
Sent: Wednesday, October 14, 2009 12:33 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Unusual bond between residues: 0 (none) and 1 (protein)

Dear namd users.

I have a question.
After generating pdb,psf file from 1JNO.pdb(Gramicidin A), the Formyl & Ethanolamine is still connected with other residues.
But when I combined the protein with lipid bilayer, the Formyl & Ethanolamine was disconnected(fall apart)
 with other residues. I searched the mailing list, and I found that John answered the similar questiojn.
But I still don't know what I should do to fix this problem. Could you give me some comments?
Thanks. -hyun.

Q: unusual bond between residues XXX and YYY.
A: "Its quite possible that you're having problems due to closely packed atoms combined with the use of a file format that doesn't provide bonding
information, in which case VMD is forced to guess and occasionally has difficulties as you describe." -John
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/2465.html

****************** combine protein with lipid bilayer *************
http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/
# STEP 5: Add Water
resetpsf

# Read in structure files
readpsf protein.psf
readpsf pope.psf

# Read in coordinates
coordpdb protein_move.pdb
coordpdb pope_move.pdb

writepsf pope_gram.psf
writepdb pope_gram.pdb

******************Output************************************
Warning) Unusual bond between residues: 0 (none) and 1 (protein)
Warning) Unusual bond between residues: 15 (protein) and 16 (none)

*************** Picture: (page 13), 4-SS03_MDMethods-4.pdf *********
I got same picture. Formyl & Ethanolamine was disconnected

http://www.google.com/url?sa=t&source=web&ct=res&cd=1&ved=0CAcQFjAA&url=http%3A%2F%2Fwww.ks.uiuc.edu%2FTraining%2FSumSchool%2Fmaterials%2Flectures%2F6-2-Intro-Protein-Structure-Dynamics%2F4-SS03_MDMethods.pdf&ei=vOfVSvXaC4mKManD0ZQD&usg=AFQjCNE2UzWRNWVWNw21vBFwp2QEidPMWg&sig2=2MCxDdMW6ibkqa-SwSXYHA

******************Topology: top_all27_prot_lipid.inp******************
# Guessed topology for N-Terminal formyl group.
RESI FOR 0.00
GROUP
ATOM HA HA .0900 !
ATOM C C .4200 !
ATOM O O -.5100 !

BOND C HA C +N
DOUBLE O C
IMPR C HA +N O
IMPR C +N HA O

****************** 1JNO.pdb******************
CONECT 1 2 3 4
CONECT 2 1
CONECT 3 1
CONECT 4 1

******************protein.psf******************
     566 !NBOND: bonds
       2 1 2 4 3 2 4 5 ...
    1022 !NTHETA: angles
       1 2 3 1 2 4 4 6 7
       4 6 18 4 2 3 5 4 2 ...
    1504 !NPHI: dihedrals
       1 2 4 5 1 2 4 6
       2 4 6 8 2 4 6 18
       2 4 6 7 3 2 4 5
       3 2 4 6 4 6 8 10
       4 6 8 14 4 6 8 9
       4 6 18 20 4 6 18 19...
      66 !NIMPHI: impropers
       2 1 4 3 2 4 1 3
       4 2 6 5 18 6 20 19...

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