VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue Feb 08 2011 - 14:49:48 CST

You want "psfcontext reset", which says exactly that. -Jim

On Tue, 8 Feb 2011, John Stone wrote:

>
> ----- Forwarded message from "Goldsmith, Jacob" <jgoldsmith_at_uky.edu> -----
>
> From: "Goldsmith, Jacob" <jgoldsmith_at_uky.edu>
> To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
> Date: Tue, 8 Feb 2011 11:11:54 -0500
> Subject: vmd-l: multiple topology files and resetpsf
>
> The problem I have is this: resetpsf does not reset the topology
> structure. I have been trying to make multiple systems of CNTs and I
> have all the peices of the system in separate .pdb files. I generally
> write my .pdb file "by hand" with a script. Is there a way to reset the
> topology structure stored? Simply reloading a different topology file
> fails. The number of atoms in the first topology file is preserved.
> Thus far, I've had to exit VMD for each separate instance.
>
> vmd > resetpsf
> clearing structure, preserving topology and aliases
>
> What I want it to say is:
> vmd > resetpsf
> clearing structure, topology, and aliases
>
> Below is my construction script for reference, run in VMD 1.8.7
>
> Thanks all,
> Jacob
>
> ####################################
> resetpsf
> topology 12nn25c.top
> # above is the topology file that changes each time
> topology ru_bi_pry.top
>
> segment BIP {
> auto angles dihedrals
> pdb ru_bi_pry.pdb
> }
> coordpdb ru_bi_pry.pdb
>
> segment NT {
> auto none
> pdb 12nn25c.pdb
> }
> coordpdb 12nn25c.pdb NT
>
> writepsf my_wonderful_md_trial.psf
> writepdb my_wonderful_md_trial.pdb
> ####################################
> # first few .pdb lines
> ATOM 1 C000 ARM 1 8.115 -0.710 -14.757 1.00 0.00 NT C
> ATOM 2 C001 ARM 1 8.115 0.710 -14.757 1.00 0.00 NT C
> ATOM 3 C002 ARM 1 7.383 3.443 -14.757 1.00 0.00 NT C
> ATOM 4 C003 ARM 1 6.673 4.673 -14.757 1.00 0.00 NT C
> ####################################
> # and ... the spacing was mutilated when I c.c.p. this below
> ####################################
> ATOM 1 RU BIPYX 1 -0.151 0.086 0.086 1.00 0.00 BIP
> ATOM 2 C10 BIPYX 1 -0.051 0.708 2.913 1.00 0.00 BIP
> ATOM 3 C6 BIPYX 1 -0.051 2.676 1.661 1.00 0.00 BIP
> ATOM 4 C9 BIPYX 1 0.087 1.378 4.109 1.00 0.00 BIP
> ATOM 5 C1 BIPYX 1 -0.221 -0.753 2.841 1.00 0.00 BIP
>
>
> ----- End forwarded message -----
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>