[gmx-users] ARG Charmm gmx 4.5.1

[Berk Hess]

Hi,

No, you should never change the charges in a force field!

Run pdb2gmx again with the -nochargegrp option.
That will make the size of all charge groups a single atom.
This will be done automatically in the 4.5.2 release which will be out soon.

Berk

Date: Fri, 17 Sep 2010 02:32:31 -0700
From: meetnahren at yahoo.com
To: gmx-users at gromacs.org
Subject: [gmx-users] ARG Charmm gmx 4.5.1

Dear Gromacs Users,

I am using plain cutoff for my 12-mer protein.
The grompp reports ARG to have a big charge group. this was also highlighted in the following mail
http://www.mail-archive.com/gmx-users@gromacs.org/msg32098.html

I was just think if changing the charges on these atoms would help,
from
13    CT2      1    ARG     CD     4        0.2     12.011   ; qtot 1.2
14     HA      1    ARG    HD1     4       0.09      1.008   ; qtot 1.29
15     HA     
 1    ARG    HD2     4       0.09      1.008   ; qtot 1.38
16    NC2      1    ARG     NE     4       -0.7     14.007   ; qtot 0.68
17     HC      1    ARG     HE     4       0.44      1.008   ; qtot 1.12
18      C      1    ARG     CZ     4       0.64     12.011   ; qtot 1.76
19    NC2      1   
 ARG    NH1     4       -0.8     14.007   ; qtot 0.96
20     HC      1    ARG   HH11     4       0.46      1.008   ; qtot 1.42
21     HC      1    ARG   HH12     4       0.46      1.008   ; qtot 1.88
22    NC2      1    ARG    NH2     4       -0.8     14.007   ; qtot 1.08
23     HC      1    ARG   HH21    
 4       0.46      1.008   ; qtot 1.54
24     HC      1    ARG   HH22     4       0.46      1.008   ; qtot 2



to




	
	
	Message body
	
	
   CD    0.18
  HD1    0.06
  HD2    0.06
   NE    -0.7
   HE    0.4
   CZ    0.6
  NH1    -0.8
 HH11    0.5
 HH12    0.5
  NH2    -0.8
 HH21    0.5
 HH22    0.5

The above transformation of charges seems reasonable.

Would like to know if this is okay...


Best,
nahren





      
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