Re: AMBER: Error on restrained MD equilibration (AMBER 7)

From: Guanglei Cui <cuigl.csb.sunysb.edu>
Date: Tue, 31 May 2005 15:02:46 -0400

Hi,

Try to put the following lines between your weight change section and
the group input section. It may help. At least it works for me when
nmropt and ntr are both used.

LISTIN=POUT
LISTOUT=POUT

Regards,

--
Guanglei
L Jin wrote:
> Thank you all for the help. I have tried to specify the group as a range and
> also using the right format of the namelist record. But it still gave the same
> error. I just need to restrain residue 1, a small molecule, in the water box to
> equilibrate the solvent. Anything else we could consider?
> 
> Cheers,
> 
> Lan
> 
> 
> 
> 
> 
>>MD heating from 0 to 300K with restraints on the solute
>> &cntrl
>>   imin = 0, ntpr = 100, ntwx = 100, ntwe = 100, ntwr = 1000,
>>   nstlim =10000, dt = 0.001,
>>   ntb = 1,cut = 8, ntr = 1, ntc = 2, ntf = 2, nmropt = 1,
>>   tempi = 0.0, temp0 = 300.0, ntt = 1, tautp = 0.5,
>> &end
>> &wt
>>   type='TEMP0', istep1=0,     istep2=500,
>>                 value1=0.0,  value2=300.0,
>>  &end
>>  &wt
>>   type='TEMP0', istep1=500,   istep2=20000,
>>                 value1=300.0, value2=300.0,
>>  &end
>>  &wt
>>   type='END',
>>  &end
>>Group input for restraint atoms
>> 10
>>RES 1 1
>>END
>>END
>>
>>
>>
>>OUTPUT:
>>
>>.....................................
>>
>>Frozen or restrained atoms:
>>     ibelly  =       0, ntr     =       1
>>
>>Molecular dynamics:
>>     nstlim  =   10000, nscm    =    1000, nrespa  =       1
>>     t       =   0.00000, dt      =   0.00100, vlimit  =  20.00000
>>
>>Temperature regulation:
>>     ig      =   71277, ntt     =       1, vrand   =       0
>>     temp0   = 300.00000, tempi   =   0.00000, heat    =   0.00000
>>     dtemp   =   5.00000, tautp   =   0.50000
>>
>>SHAKE:
>>     ntc     =       2, jfastw  =       0
>>     tol     =   0.00001
>>
>>NMR refinement options:
>>     iscale  =       0, noeskp  =       1, ipnlty  =       1, mxcub   =
>>1
>>     scalm   = 100.00000, pencut  =   0.10000, tausw   =   0.10000
>>
>>Ewald parameters:
>>     verbose =       0, ew_type =       0, nbflag  =       1, use_pme =
>>1
>>     vdwmeth =       1, eedmeth =       1, frc_int =       0, netfrc  =
>>1
>>     Box X =   41.027   Box Y =   40.420   Box Z =   40.470
>>     Alpha =   90.000   Beta  =   90.000   Gamma =   90.000
>>     NFFT1 =   48       NFFT2 =   40       NFFT3 =   40
>>     Cutoff=    8.000   Tol   =0.100E-04
>>     Ewald Coefficient =  0.34864
>>     Interpolation order =    4
>>
>>    LOADING THE CONSTRAINED ATOMS AS GROUPS
>>
>>
>>   5.  REFERENCE ATOM COORDINATES
>>
>>
>>    ----- READING GROUP     1; TITLE:
>> MD heating from 0 to 300K with restraints on the solute
>>
>>     rfree: Error decoding variable  1  3 from:
>> &cntrl
> 
> 
> 
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Received on Tue May 31 2005 - 20:53:01 PDT