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

From: Jérôme Hénin (
Date: Fri May 31 2013 - 10:30:01 CDT

Some angle parameters may be missing after patching. Just in case, check the "Regen" option in the AutoPSF documentation.


----- 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
> . 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

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