Would I only include the &wt type="end" portion? If I don't have any
&wt, it won't run through sander.
When I look at the output, it says that it read in the restraints:
------------------------------------------------------------------------
------
3. ATOMIC COORDINATES AND VELOCITIES
------------------------------------------------------------------------
--------
begin time read from input coords = 0.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
REST 0 10000 1.000000 1.000000 0 0
RESTRAINTS:
Requested file redirections:
DISANG = enzph1alarestraints.f
Restraints will be read from file: enzph1alarestraints.f
Here are comments from the DISANG input file:
# distance restraints prepared by hand for Ca
#( oxygen 1 Calcium upper bound)
#
# 79 GLY O 171 CA CA 2.8
#
Number of restraints read = 4
Done reading weight changes/NMR restraints
But each step says the following:
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
0.000
Did I set something incorrectly? It doesn't look like it's actually
restraining anything.
Thanks,
Kara Di Giorgio
On Apr 12, 2005, at 9:09 AM, Carlos Simmerling wrote:
> I don't think you need to use the weight change on REST if it isn't
> changing.
>
> look at the output file- does it properly read the restraints? when
> the Ca moves,
> does the restraint energy change? read the output carefully, it should
> tell you what's going on.
>
> Kara Di Giorgio wrote:
>
>> I'm not sure if I formatted everything correctly. It ran, but the
>> calcium that I'm trying to restrain is still leaving the protein
>> after 8 ps like the restraints weren't there at all. Could someone
>> look at my md.in and restraints.f files to see if they can see
>> anything majorly incorrect? I'll include them in this message.
>>
>> Thanks,
>>
>> Kara Di Giorgio
>>
>>
>> *md.in*
>>
>> stromelysin and ph1ala MD G4eneralised Born, 12 angstrom cut off Ca
>> restraints
>> &cntrl
>> imin = 0, ntb = 0,
>> igb = 1, ntpr = 100, ntwx = 100,
>> ntt = 3, gamma_ln = 1.0,
>> tempi = 300.0, temp0 = 300.0
>> nstlim = 10000, dt = 0.001,
>> nmropt = 1,
>> cut = 12
>> /
>> &wt type="REST", istep1=0, istep2=10000, value1=1.0, value2=1.0,
>> /
>> &wt type='end'
>> /
>> DISANG = enzph1alarestraints.f
>>
>>
>> *restraints.f*
>>
>> # distance restraints prepared by hand for Ca
>> #( oxygen 1 Calcium upper bound)
>> #
>> # 79 GLY O 171 CA CA 2.8
>> #
>> &rst iat= 1278, 2611, r3=2.8, r4= 3.3, ialtd=0, /
>> #
>> # 76 ASP OD1 171 CA CA 2.8
>> #
>> &rst iat= 1247, 2611, r3=2.8, r4= 3.3, ialtd=0, /
>> #
>> # 77 GLY O 171 CA CA 2.8
>> #
>> &rst iat= 1257, 2611, r3=2.8, r4= 3.3, ialtd=0, /
>> #
>> # 102 GLU OE2 171 CA CA 2.8
>> #
>> &rst iat= 1585, 2611, r3=2.8, r4= 3.3, ialtd=0, /
>
>
>
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Received on Tue Apr 12 2005 - 18:53:00 PDT
