AMBER Archive (2005)

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

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Wed Jun 01 2005 - 09:18:37 CDT

Hi, Lan

Here's my input (see attachment). Hope it helps. Another way around this
is to take advantage the atommask feature in sander8. See restraintmask
in the manual for details.

Regards, 

--
Guanglei

L Jin wrote:
> Hi Guanglei,
> 
> Thank you for the suggestion but it does not work in my case. Could you send me
> your input file if possible for me to find some clue?
> 
> Lan
> 
> 
> 
> 
> Quoting Guanglei Cui <cuigl_at_csb.sunysb.edu>:
> 
> 
>>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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> 
> 
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md5.in - DB3 antibody
 &cntrl
        imin = 0, ntx = 7, nstlim = 1000000,
        ntc = 2, ntf = 1, tol=0.0000001, ntt = 1, dt = 0.002,
        ntb = 2, ntp = 1,
        ntwx = 1000, ntwe = 0, ntwr = 10, ntpr = 10,
        scee = 1.2, cut = 8.0, npscal = 1,
        ntr = 1, ibelly = 0, temp0 = 300.0, temp0les = 250.00,
        nscm = 1000, iwrap = 0, irest = 1, nmropt = 1,
 &end
 &wt
        TYPE="DUMPFREQ", istep1=10,
 &end
 &wt
        TYPE="END",
 &end
DISANG=pmf.rst.1
DUMPAVE=pmfdump_400.noq.fullq
LISTIN=POUT
LISTOUT=POUT
 group input
 0.1
 FIND
 CA * * *
 C * * *
 N * * *
 O * * *
 SEARCH
 RES 1 719
 END
END

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