ibelly means that the atoms are fixed in space. it is not involved
in the energy or force calculations. restraints refer
to an extra term that you put in the force field. this gives
an energy and force.
500 kcal/mol is probably too high for a restraint. try something
much weaker or the dynamics may be unstable.
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
===================================================================
Mayumi Haga wrote:
>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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>
>
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Received on Tue Feb 08 2005 - 13:53:01 PST
