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.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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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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Received on Wed Jun 01 2005 - 15:53:00 PDT