Quoting Bill Ross <ross.cgl.ucsf.EDU>:
>> It works with nstlim = 100000 and position constraint 10.0.
>
> You are saying it crashes on nstlim = 10000 but runs ok with
> nstlim = 100000, for the same restraint energy of 10? This does
> not make sense.
>
I was wrong, it works also with 10000.
>> But I found the carbon atoms are moving a lot
>
> What kind of movement? (I see you are using constant volume, so
> coordinate scaling would not be involved as it would be for
> constant pressure.)
>
The six membered-like rings doesn't exist even though the actual
monomer is the two carbon molecule.
>> (I didn't make bonds
>> between the residues which have 2 carbon atoms because leap generates
>> weird bonds longer than about 5~10 A)
>
> That implies you bonded the wrong atoms. Bonding a whole sheet of carbons
> seems like it would be difficult to get right, but possible. You need to
> know how to name your residues/atoms for the bonds. Be sure to develop
> the setup as a script for replicability.
I attached prepi and the original two-carbon monomer pdb file.
And I used the following script in leap
================================================
source leaprc.ff99SB
source leaprc.gaff
loadamberprep c2.prepi
gr=loadpdb 20.pdb
##bondByDistance gr 1.5
savepdb gr 20amb.pdb
solvatebox gr TIP3PBOX {0 0 20}
saveamberparm gr 20.prmtop 20.inpcrd
=================================================
>
>> and I gave 10->5000 and NaN
>> error was coming out again.
>
> For the restraint weight? 5000 is very high, you could try 50.
I tried 50, but it also gave me NaN error.
> Also, I will suggest gradual warming again.
>
>> Do you think this structure setup is wrong?
>
> I can't tell. E.g. you haven't described your residue unit.
>
The residue design looks like:
-===========================
ATOM 0 C GRA 0 0.000 0.000 0.000
ATOM 1 C1 GRA 0 -0.000 1.421 0.034
TER
ATOM 2 C GRA 1 2.461 0.000 0.000
ATOM 3 C1 GRA 1 2.461 1.421 0.034
TER
ATOM 4 C GRA 2 1.230 2.131 0.000
ATOM 5 C1 GRA 2 1.230 3.552 0.034
TER
ATOM 6 C GRA 3 -0.000 4.263 0.000
ATOM 7 C1 GRA 3 -0.000 5.684 0.034
TER
==========================================
Thank you.
Bongkeun Kim
>
>
>> Thank you.
>> Bongkeun Kim
>
>> Quoting Bill Ross <ross.cgl.ucsf.EDU>:
>
>> >> &cntrl
>> >> imin = 0,
>> >> irest = 0,
>> >> ntx = 1,
>> >> ntb = 1,
>> >> cut = 10.0,
>> >> ntr = 1,
>> >> ntc = 2,
>> >> ntf = 2,
>> >> tempi = 0.0,
>> >> temp0 = 300.0,
>> >> ntt = 3,
>> >> gamma_ln = 1.0,
>> >> nstlim = 10000, dt = 0.002
>> >> ntpr = 50, ntwx = 100, ntwr = 1000
>> >> /
>> >> Hold the graphite fixed
>> >> 10.0
>> >> RES 1 120
>> >> END
>> >> END
>> >
>> > You are warming the waters rapidly from 0 to 300K - you could
>> > try warming slower.
>> >
>> > Bill
>> >
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>> >
>
>
>
>
>
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- application/download attachment: 2c.pdb
Received on Wed Oct 20 2010 - 11:30:07 PDT
