AMBER Archive (2005)

Subject: AMBER: again: F, Cl, Br, I in MMPBSA

From: Yong Xu (yxu_at_mail.sioc.ac.cn)
Date: Fri Oct 14 2005 - 22:07:59 CDT

Dear Prof. Case, and Prof Junmei Wang

I use AMBER7.0 version.
I want to do some MMPBSA research on a series of small molecules composed of F, Cl, Br, or I atoms.
but there are no parameter for those elements.when I do MMPBSA analysis, there are no surface area.
what's the problem?
where can I find the necessary parameter?

and furthermore, what should be added in my_amber94_delphi.crg, my_parse_delphi.siz and atmtypenumbers files?

Although there are some question and answer in the mailing-list, but there are no complete and standard paramenter for this kind of atoms. I think this problem is a very universal problem for some new-user.

I will be very appreciated for any reply

Best regard!

Yong Xu
yxu_at_mail.sioc.ac.cn
2005-10-15

===========================================================
* Yong Xu
* State Key Lab of Bioorganic & Natural Product Chemistry
* Shanghai Institute of Organic Chemistry
* Chinese Academy of Science
           
* 354 Feng Lin Road, Xu Hui District
* Shanghai, 200032, China
        
* Email: yxu_at_mail.sioc.ac.cn
* xuyongch_at_yahoo.com
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