AMBER Archive (2005)

Subject: AMBER: TI in Amber8

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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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• Previous message: Zhang Bing: "AMBER: New problem of parallel sander"
• Next in thread: David A. Case: "Re: AMBER: TI in Amber8"
• Reply: David A. Case: "Re: AMBER: TI in Amber8"
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