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

From: Yize Hu (yizehu_at_gmail.com)
Date: Fri May 31 2013 - 10:20:52 CDT

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
Tel: +8615951812537
Address:  Room 5B447, Nanjing University Xianlin Campus, 163 Xianlin Dadao,
Nanjing 210046, China

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:16 CST