Previous Thread
Next Thread
Print Thread
partial charges from paramchem
#32793 10/21/13 09:21 AM
Joined: Jun 2013
Posts: 15
L
ldarre Offline OP
Forum Member
OP Offline
Forum Member
L
Joined: Jun 2013
Posts: 15
Hi,
If for a new compound, paramchem indicate that a few partial charges have high penalties but for the rest of the atoms the penalty is below 10 or even zero, is it recommendable to only parametrize the high penalty charges while fixing the rest of the atomic charges in the low penalty values proposed by paramchem? or all the charges should be parametrized?

Thans a lot

Re: partial charges from paramchem
ldarre #32799 10/21/13 05:37 PM
Joined: Dec 2005
Posts: 1,535
Forum Member
Offline
Forum Member
Joined: Dec 2005
Posts: 1,535
It is difficult to provide a general answer to these kind of questions; they should be looked at on a case-by-case basis. Roughly spoken, the standard CHARMM charge optimization procedure requires breaking up the molecule into relevant fragments first, as shown in the CGenFF paper and tutorials and briefly explained in the FAQ. If the high penalties (how high are they exactly?) are located at the interface between 2 fragments / groups, then it doesn't seem to be worth trying to optimize them. If they are within a group, then it might be worth optimizing that group (ie. all its charges).

I know it's very vague of me to say "relevant fragments", but this cannot easily be explained in a few sentences; that's exactly why I started with stating that it is difficult to provide a general answer.

Re: partial charges from paramchem
ldarre #32812 10/22/13 10:43 AM
Joined: Jun 2013
Posts: 15
L
ldarre Offline OP
Forum Member
OP Offline
Forum Member
L
Joined: Jun 2013
Posts: 15
Hi,
I understand the difficulty on giving a general answer but still your reply is a really useful guideline on how to think about this problem.
As it was just a general doubt that I came up with I do not have any exact penalty to refer to, but I was thinking in >50 values.

Thanks again.


Moderated by  alex, lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.013s Queries: 20 (0.006s) Memory: 0.9025 MB (Peak: 0.9777 MB) Data Comp: Off Server Time: 2020-08-09 00:12:18 UTC
Valid HTML 5 and Valid CSS