VMD-L Mailing List
From: laura (stting0718_at_eyou.com)
Date: Wed Mar 05 2008 - 02:33:41 CST
- Next message: Fei Chen: "What's the main reason of the structure or function of a protein?"
- Previous message: John Stone: "Re: Visualizing trajectory with changing atoms"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
Hi all,
When I use the paratool to compute the missing Charmm parameters, something puzzle me.
First is the Charmm charge. I transfer some "group" charges which is the existing Charmm molecule to the fragment model, and then, adjust the charges upon linking the group to form fragment model. I don't know whether this is reasonable.
Second is about the results. I find there are some different parameters corresponding to the same type of bond or angle.
For example, in the group of
/H1
C-C
\H2
the parameter of "C-C-H1" and "C-C-H2" is different. The same group in different positions of the whole molecule also corresponds to different
parameter.
How to control these parameters? Can I use the average of them?
Thank you for any help!
laura
--外国货也超便宜!
--http://freemail5.eyou.com/sys_sig.php?url=aHR0cDovL2V5b3VhZnAuYWxseWVzLmNvbS9tYWluL2FkZmNsaWNrP2RiPWV5b3VhZnAmYmlkPTk1LDgxLDMmY2lkPTczLDksMSZzaWQ9MTY4JmFkdmlkPTQmY2FtaWQ9NCZzaG93PWlnbm9yZSZ1cmw9aHR0cDovL2FkZmFybS5tZWRpYXBsZXguY29tL2FkL2NrLzQwODAtMjI5MDMtOTQ5OS0wP2FpZD1leW91O3RleHQ7MTAzJm1wcm89aHR0cDovL3BhZ2VzLmViYXkuY29tLmNuL3dvcmxkYnV5L3VzYS5odG1s
--http://sms.eyou.com
--无忧二二族、足球大富翁...尽在亿邮短信
- Next message: Fei Chen: "What's the main reason of the structure or function of a protein?"
- Previous message: John Stone: "Re: Visualizing trajectory with changing atoms"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
