AMBER: How to calculate RESTRAINT value

From: Mayumi Haga <haga.cir.tohoku.ac.jp>
Date: Tue, 8 Feb 2005 13:09:25 +0900

Dear AMBERs

Thank you for your reply about the PDB file problem.

By the way, Now I have another question.

I've been using IBELLY to fix my artificial substrate, but I cannot find any
restraint value in my out file.

i.e.
 
---------------------------------------------------------------------------- 
--
 NSTEP =      200   TIME(PS) =      20.400  TEMP(K) =   288.55  PRESS =
-167.9
 Etot   =    -81669.4049  EKtot   =      9576.5618  EPtot      =
-91245.9667
 BOND   =        34.2236  ANGLE   =       135.0292  DIHED      =
424.4497
 1-4 NB =       163.0840  1-4 EEL =      -346.2644  VDWAALS    =
6859.9586
 EELEC  =    -98516.4473  EHBOND  =         0.0000  RESTRAINT  =
0.0000
 EKCMT  =      4775.1764  VIRIAL  =      5758.1465  VOLUME     =
271079.8105
                                                    Density    =
0.8623
 Ewald error estimate:   0.3374E+00
 
----------------------------------------------------------------------------
--
so I use NTR=1 and the force value is 500kcall/mol to fix my substrate, the
restraint value exists in my out file
 
----------------------------------------------------------------------------
-----
NSTEP =      250   TIME(PS) =      20.500  TEMP(K) =   294.29  PRESS =
-2224.7
 Etot   =   -145992.9976  EKtot   =     12405.0228  EPtot      =
-158398.0204
 BOND   =      1204.0353  ANGLE   =      6599.9700  DIHED      =
15895.2334
 1-4 NB =      -192.8316  1-4 EEL =     16774.5700  VDWAALS    =
13884.7905
 EELEC  =   -214269.8161  EHBOND  =         0.0000  RESTRAINT  =
1706.0283
 EAMBER (non-restraint)  =   -160104.0487
 EKCMT  =      5418.5360  VIRIAL  =     19002.5551  VOLUME     =
282804.1500
                                                    Density    =
0.9117
 Ewald error estimate:   0.8948E-01
 
----------------------------------------------------------------------------
--------
Does it mean that the value of RESTRAINT is only depended on NTR?
It doesn't have any relationship with IBELLY?
Will you tell me what command in sander will effect the calculation of  the
RESTRAINT value? 
Sincerely yours,
Mayumi
******************************************************************
Mayumi Haga
Kawano Laboratory, Center for Interdiscipinary Research,
Tohoku University, Japan
*******************************************************************
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Received on Tue Feb 08 2005 - 04:53:01 PST
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