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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Received on Fri Jun 03 2005 - 11:53:00 PDT
