VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Dec 05 2006 - 15:57:09 CST

Hi Mohamed,
when building the lipid segment using psfgen, you should add the commands
first NONE
last NONE
to your segment statement, eg,

segment A {
pdb lipids.pdb
first NONE
last NONE
}

This will avoid attempts to apply the default nter/cter patches.
Peter

Mohamed Osman wrote:
> 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