VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Sat Sep 08 2007 - 21:56:51 CDT

Atoms are guessed at the origin when the topology file does not provide
enough information in "IC" records to guess coordinates based on other
atoms. This is the case if the atoms do not appear as the first or last
atom listed in an IC record. (Hydrogens are the exception, and are
guessed using some simple rules if necessary.) You can probably add an IC
record to fix the problem.

>From memory, the format of the IC record is something like:

IC atom1 atom2 atom3 atom4 bond1-2 angle1-2-3 dihedral 1-2-3-4 angle2-3-4 bond3-4

-Jim

On Wed, 5 Sep 2007, maria goranovic wrote:

> Hi,
>
> I have coordinates of the choline headgroup of a PC lipid from a crystal
> structure, and am trying to use psfgen to guess the coordinates of the rest
> of the lipid molecule
>
> The guessing goes very well, except that for some reason, two of the
> carbonyl atoms (one in each alkyl chain) are guessed to be at the origin
> (0,0,0); quite far away from the rest of the molecule. Can anyone tell me
> what I am doing wrong ?
>
> Here is the script being used. The file pop1.pdb has the coordinates of
> choline.
>
> ############
> resetpsf
> package require psfgen
> topology top-combined.rtf
>
> segment POP1 {
> first none
> last none
> pdb pop1.pdb }
> coordpdb pop1.pdb POP1
>
> guesscoord
> regenerate angles dihedrals
>
> writepdb popc-only.pdb
> writepsf popc-only.psf
> ############
>
> Thank you
>
> -Maria
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>