VMD-L Mailing List

From: Mohamed Osman (osman_at_eecs.wsu.edu)
Date: Tue Dec 05 2006 - 15:45:45 CST

I am making a psf file for a lipid strating from pdb file for a solavted
lipid.
As the message below shows, it is looking for N-terminals and C-terminals.
When I examined the resulting pdb file, I found additional atoms at the
beginning of the file: (see below)
The input pdb starts at N4 (line 7).

How can I tell it is alipid and not protein to avoid the warnings? and
adding of the additional lines ??
c----------------------------------------------------------------------
building segment L
reading residues from pdb file pope_LIP.pdb
extracted 128 residues from pdb file
Info: generating structure...
no atom C in residue POP:1 of segment L
Warning: add conformation failed in patch NTER
no atom CA in residue POP:128 of segment L
Warning: add improper failed in patch CTER
no atom CA in residue POP:128 of segment L
Warning: add conformation failed in patch CTER
no atom N in residue POP:128 of segment L
Warning: add conformation failed in patch CTER
Info: segment complete.
reading coordinates from pdb file pope_LIP.pdb for segment L

----------------------------------------------------------------------------------Output
pdb:----------------------------
REMARK original generated coordinate pdb file
ATOM 1 N POP A 1 0.000 0.000 0.000 -1.00 0.00 L
N
ATOM 2 HT1 POP A 1 0.000 0.000 0.000 -1.00 0.00 L
H
ATOM 3 HT2 POP A 1 0.000 0.000 0.000 -1.00 0.00 L
H
ATOM 4 HT3 POP A 1 0.000 0.000 0.000 -1.00 0.00 L
H
ATOM 5 CA POP A 1 0.000 0.000 0.000 -1.00 0.00 L
C
ATOM 6 HA POP A 1 0.000 0.000 0.000 -1.00 0.00 L
H
ATOM 7 N4 POP A 1 40.717 45.100 15.740 1.00 0.00 L
N

Thanks

Mohamed Osman