Re: A fancy problem in calculating the protonated glutamic acid modelled by adding the patch of GLUP

From: Yize Hu (yizehu_at_gmail.com)
Date: Sat Jun 01 2013 - 03:17:27 CDT

Dear Jerome,

I am really grateful for your concise but accurate suggestion. Now the
simulation runs correctly!

Best,

Yize

On Fri, May 31, 2013 at 11:30 PM, Jrme Hnin <jerome.henin_at_ibpc.fr> wrote:

> Some angle parameters may be missing after patching. Just in case, check
> the "Regen" option in the AutoPSF documentation.
>
> Cheers,
> Jerome
>
>
> ----- Original Message -----
> >
> >
> >
> > Hello everyone:
> > When I am using NAMD 2.9 (2012-4-30) and CHARMM27 force field to
> > calculate the protonated GLU amino acid, I found a very strange
> > problem. (The protonated GLU was modelled by the autopsf plugin in
> > VMD, the patch of GLUP was attached on the GLU molecule to get a
> > protonated side chain end.)
> > The H-O-C angle on the COOH of its side chain became around 9 degree
> > at the end of minimization.
> > I think the angle parameter of line 650 (H OH1 CD) in the par file
> > should be the one used in calculating the angle energy term. So I
> > tried to replace the Theta0 of H OH1 CD with a value of zero to see
> > what will happen. But the result remains the same. And problem
> > remains when the Theta0 value of H OH1 CD is changed to 100000. But
> > the replacement appears that the program ignored the angle parameter
> > of H OH1 CD.
> >
> > I also tried NAMD 2.8. Problem remains. And ASPP patch also has the
> > same problem (while CNEU patch works well). I am really confused. Is
> > there any deep mistakes in my configuration?
> > The simulation files can be got at
> >
> https://docs.google.com/file/d/0BzhQA08dpDwbQnVMU09sVHVoM2s/edit?usp=sharing
> > . Thank you very much for your kind help!
> >
> >
> > --
> > Hu Yize
> > Kuang Yaming Honors School
> > Nanjing University
> > China
> >
> > Tel: +8615951812537
> >
> > Address: Room 5B447, Nanjing University Xianlin Campus, 163 Xianlin
> > Dadao, Nanjing 210046, China
>

-- 
Hu Yize
Kuang Yaming Honors School
Nanjing University
China
Tel: +8615951812537
Address:  Room 5B447, Nanjing University Xianlin Campus, 163 Xianlin Dadao,
Nanjing 210046, China

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