AMBER Archive (2005)

Subject: AMBER: How to calculate RESTRAINT value

From: Mayumi Haga (haga_at_cir.tohoku.ac.jp)
Date: Mon Feb 07 2005 - 22:09:25 CST


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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