From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Thu Dec 22 2005 - 21:01:31 CST
Hi Shirley,
I use the OPLS force field, so I actually do not have a topology file, and
I don't want to create one. I use Alessandro Pedretti's Vega ZZ to create
all my .psf files. I load in a .pdb FAT formatted file. It contains all
of the usual .pdb coordinate info and atom names, but it also contains
information about connectivity in the CONECT records as well as the
charges and atom types that link your .pdb file to your parameter file.
There is a nice description of this format in the manual found on the
webpage. I love it because I just build one .pdb FAT file for each
molecule I am using. Then I can replicate it on a lattice in VEGA ZZ and
simulate as many as I want.
Vega ZZ is free for academic use and can be downloaded for Windows at
http://users.unimi.it/~ddl/vega/index3.htm
It also has a lot of other useful tools, including a solvation tool which
allows you to solvate with anything. You can put in your own solvents.
You can save your .pdb (nonstandard with only the coordinate info which is
all NAMD needs) and the XPLOR formatted .psf file directly from Vega ZZ
and start your simulation.
Hope this helps.
Josh
On Thu, December 22, 2005 8:01 pm, Shirley Li wrote:
> Dear Josh,
>
> Thank you very much for detailed information. Indeed, it is the presence
> of the HT-HT bond specification in the topology file. I have made the
> changes as Peter suggested. It works now.
>
> Yes, I used the topology file to create the .psf, specifically, with
> PSFGEN. I have a question here based on you message: are there also
> other good ways of generating .psf file besides using PSFGEN?
>
> Thank you again for your help.
>
> Shirley
>
>
>
> "Joshua D. Moore" <jdmoore_at_unity.ncsu.edu> wrote: Peter's last email
> described the changes you need to make to the TIP3
> topology files. You are using the topology file to generage your psf?
>
> I am saying this from memory, but a few months ago I looked all this up.
> If you specify a HT-HT bond length only and not a HT-OT-HT angle, then the
> HT-HT bond length with be used to fix the H-H length in water. If the
> HT-OT-HT angle is present at all (even if the HT-HT bond length is
> specified) it is used for the rigid bond calculation. The HT-HT bond
> length in this case is ignored. However, you will still get an error if
> you have HT-HT bonds (and HT-HT-OT angles) in your .psf file and you don't
> specify the HT-HT parameter in your parameter file. So I don't use the
> HT-HT length when generating my .psf file and I always just use the
> HT-OT-HT angle. This ensures that my .psf file is correct and that I
> don't need a HT-HT parameter in my parameter file.
>
> Josh
>
> The HT-HT-OT angle is not needed and doesn't exist really. It is
> generated in the .psf like Peter said because you have a HT-HT bond in the
> topology.
>
>
> --------------------------------------------------
> Joshua D. Moore
> Graduate Student
> North Carolina State University
> Department of Chemical and Biomolecular Engineering
> Box 7905 Centennial Campus
> Engineering Building I
> 911 Partners Way
> Raleigh, NC 27695-7905
> Phone: (919) 513-2051
> Fax: (919) 513-2470
> Email: jdmoore_at_unity.ncsu.edu
> --------------------------------------------------
>
>
>
>
>
> ---------------------------------
> Yahoo! for Good - Make a difference this year.
--------------------------------------------------
Joshua D. Moore
Graduate Student
North Carolina State University
Department of Chemical and Biomolecular Engineering
Box 7905 Centennial Campus
Engineering Building I
911 Partners Way
Raleigh, NC 27695-7905
Phone: (919) 513-2051
Fax: (919) 513-2470
Email: jdmoore_at_unity.ncsu.edu
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