From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Thu Dec 22 2005 - 18:03:57 CST
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.
On Thu, December 22, 2005 3:57 pm, Shirley Li wrote:
> Dear NAMD expert,
>
> I was running minimization with NAMD. It crashed with the complaint of
> the HT-HT-OT angle parameter. I checked the NAMD parameter file and saw
> that only HT-OT-HT angle param is provided for TIP3, not HT-HT-OT. I
> wonder if the HT-HT-OT is needed in general. In my case, should I add
> the HT-HT-OT angle to the parameter file?
>
> Any information/comment will be greatly appreciated. BTW, my system has
> both crystal water and solvent, both with the same resname "TIP3" while
> different segname.
>
> Shirley
>
>
> ---------------------------------
> Yahoo! for Good - Make a difference this year.
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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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