AMBER Archive (2005)

Subject: AMBER: TI in Amber8

From: 建平 胡 (lion_hjp_at_yahoo.com.cn)
Date: Fri Jun 03 2005 - 04:49:02 CDT


 
Hi, Amber 8 user:

I am a new Amber8 user. In amber 8 manual , I find there is only TI in amber 8 ,but FEP can not be used. What I said is true? When following the FEP/TI example" Valine to Alaine Free Energy determination" in internet web, But I can not get the right result. I think there are some errors in my frcmod file (I don’t know the 2nd and 5th column item meaning )and the operation in Xleap (especially the charge item). There are two files as follow:

(1)Frcmod file :

remark goes here

MASS

DH 1.008

BOND

HC-DH 0 0

ANGLE

DH-HC-DH 0.0 0.0

CT-HC-DH 0.0 0.0

DIHEDRAL

HC-CT-CT-CT 4 5.70 60.0 2.000

DH-HC-CT-HC 1 0 0 2.000

CT-CT-CT-HC 4 5.70 60.0 2.000

HC-CT-HC-DH 1 0 0 2.000

HC-CT-CT-HC 4 5.70 60.0 2.000

CT-CT-HC-DH 1 0 0 2.000

IMPROPER

NONBON

DH 0.000 0.00

(2)the essential content in xleap

In conpute the delta.charge. I use Val system to minus Ala system(the essential mutation is CH(CH3)2 in Val to CH3 in Ala). In Amber 8 topo-base I get the Ala charge .CH3(-0.1825, 0.0603, 0.0603, 0.0603), so for example: the first delta.charge = 0.2985-(-0.1825)= 0.491.

Name

Type

charge

element

unused

Pert.name

Pert.tye

Delta.charge

CB

CT

0.2985

C

true

CB

CT

0.491

HB

HC

-0.0297

H

True

HB

HC

-0.09

CG1

CT

-0.3192

C

True

CG1

HC

-0.3795

HG11

HC

0.0791

H

True

HG11

DH

0.0791

HG12

HC

0.0791

H

True

HG12

DH

0.0791

HG13

HC

0.0791

H

True

HG13

DH

0.0791

CG2

CT

-0.3192

C

true

CG2

HC

-0.3795

HG21

HC

0.0791

H

true

HG21

DH

0.0791

HG22

HC

0.0791

H

True

HG22

DH

0.0791

HG23

HC

0.0791

H

true

HG23

DH

0.0791

Follow the ideal above, But I gain a wrong result ,DV/DL approximately equal to 110. I don’t know how to correct it. Please give me some suggestions for this question .

thank you in advance

huhu

                
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