VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Feb 16 2004 - 17:55:50 CST

Hi,

The easy way is to use a Tcl foreach loop over all of your segments.
I've attached a script I used to build a DPPC patch from similar input.
There is some extra code to replicate the lipids, but otherwise this is a
full example.

Also, be sure to use "regenerate angles dihedrals" after building all of
the lipid segments or you'll be missing several angles and dihedrals.

-Jim

On Mon, 16 Feb 2004, Satyavani Vemparala wrote:

>
> I have a DOPC coordinate file (PDB) in which the residue numbers is
> repeating. i.e.,
>
> side chains (OLEO) have residue numbers 1 & 3
> the head group (PCGL) has residue number 2
>
> and this repeats for all the lipid molecules (the last entry in every
> column has the the information about the lipid number e.g.,:
>
> ATOM 1 C1 OLEO 1 25.238 -18.360 17.677 0.00 0.00 L001
> ATOM 139 C1 OLEO 1 -10.888 -25.455 14.071 0.00 0.00 L002
>
> when iam trying to use psfgen to generate psf files, it does that only for
> the first lipid molcule and gives errors for all the other lipids:
>
> building segment U1
> reading residues from pdb file dopc-h.pdb
> duplicate residue key 1
> ERROR: failed on residue OLEO from pdb file
> duplicate residue key 2
> ERROR: failed on residue PCGL from pdb file
> duplicate residue key 3
>
> I guess the tedious way is to seperate each segment into a pdb file and
> then use psfgen (in which segment info is to be repeated 72 times!)
>
> But i was wondering if there is an easier way out of it.
>
> Thanks
> vani
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