VMD-L Mailing List

From: Jiawei Xu (jix20.forward_at_gmail.com)
Date: Thu Jan 10 2013 - 11:30:40 CST

Hi,

In the psf file, the element type, such as CG2R61 and HGR61, usually
from column 30 as following:

   25521 D1 1 PFL CG CG2R61 -0.230000 12.0110 0

   25522 D1 1 PFL HG HGR61 0.140000 1.0080 0

However, since CG2R61 is a little bit longer name, when calculate the
charge on CG as following in VMD, it gave a wrong number:

set charge [vecsum [$cg get charge]]

CG2R61: 1.0 # not -0.23 but read the number "1" in "CG2R61",
reading the character on column 35.

HGR61 : 0.14

If modifying the psf file as the following, (move CG2R61 one column
left) it gave the right charge for CG CG2R61. However, the element
type of CG2R61 start from column 29 now (no as usual).

   25521 D1 1 PFL CG CG2R61 -0.230000 12.0110 0

   25522 D1 1 PFL HG HGR61 0.140000 1.0080 0

set charge [vecsum [$cg get charge]]

CG2R61: -0.23

I am wondering if it will cause problem in NAMD calculations?
I am wondering if there is a better way to solve this problem.
I am wondering where I can find the explanation of the EXACT format of
psf file. By the way, the content in
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node21.html
is not enough.

Thanks very much! 

-- 
Jiawei Xu