AMBER Archive (2006)

Subject: AMBER: charge problem in MM-PBSA

From: linfu (linfu3200_at_mail.sioc.ac.cn)
Date: Tue Dec 19 2006 - 19:53:52 CST

Dear Amber Community!

i calculate binding free energy of two small molecules using MM-PBSA in Amber7 package.
here my problem is how modify the charge file(my_amber94_delphi.crg)
first i use this one
!Amber parm94 charges
atom__resnumbc_charge_
CBM FRO -0.181
H32 FRO 0.097
H33 FRO 0.097
CBL FRO -0.226
CBN FRO -0.271
H31 FRO 0.152
. . .
. . .
. . .
H45 MOL 0.072
H39 MOL -0.060
CAC MOL -0.332
H40 MOL 0.072
H41 MOL 0.072
H42 MOL 0.072
**********************************************************
then i use another charge file
!Amber parm94 charges
atom__resnumbc_charge_
CBM FRO 1 -0.181
H32 FRO 1 0.097
H33 FRO 1 0.097
CBL FRO 1 -0.226
CBN FRO 1 -0.271
H31 FRO 1 0.152
. . .
. . .
. . .
H45 MOL 2 0.072
H39 MOL 2 -0.060
CAC MOL 2 -0.332
H40 MOL 2 0.072
H41 MOL 2 0.072
H42 MOL 2 0.072
**********************************************************
however, after calcultion, the result is not the same.
So i am really confused! Could anyone help me point out
which charge file(my_amber94_delphi.crg) is correct.
Thank you very much!

BEST REGARDS
Fu Lin

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu