Besides PSFGEN, are there any other good ways of generating .psf file

From: Shirley Li (
Date: Thu Dec 22 2005 - 19:01:36 CST

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.

"Joshua D. Moore" <> 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.


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

Joshua D. Moore
Graduate Student
North Carolina State University
Department of Chemical and Biomolecular Engineering
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Engineering Building I
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Raleigh, NC 27695-7905
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