# Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials"

From: Ƚͦ <rantingjing0445019.gmail.com>
Date: Wed, 2 Oct 2013 18:52:36 +0800

Dear Prof. David A Case,

I followed the strategy as above.
When I run the md simulation, I met a new problems.
Softcore Mask :136.O,H1,H2; matches 3 atoms
this run corresponds to V0, its softcore atoms interact fully for
lambda=0
this process: 26292 atoms, partner process: 26289 atoms
Checking for mismatched coordinates.
WARNING: Local coordinate 1 differs from partner coordinate 1 !
Deviation is small, changing partner coordinate.
WARNING: Local coordinate 2 differs from partner coordinate 2 !
Deviation is small, changing partner coordinate.
WARNING: Local coordinate 3 differs from partner coordinate 3 !
Deviation is small, changing partner coordinate.
WARNING: Local coordinate 4 differs from partner coordinate 4 !
Deviation is small, changing partner coordinate.
WARNING: Local coordinate 5 differs from partner coordinate 5 !
Deviation is small, changing partner coordinate.
WARNING: Local coordinate 6 differs from partner coordinate 6 !
Deviation is small, changing partner coordinate.
WARNING: Local coordinate 7 differs from partner coordinate 7 !
Deviation is small, changing partner coordinate.
WARNING: Local coordinate 8 differs from partner coordinate 8 !
Deviation is small, changing partner coordinate.
WARNING: Local coordinate 9 differs from partner coordinate 9 !
Deviation is small, changing partner coordinate.
WARNING: Local coordinate 6598 differs from partner coordinate 6589 !
Atom coordinate disagreement
Check input files.

for V1 state, the erro is the same

my inputfile is for V0:
density equilibration
&cntrl
imin=0, irest=0, ntx=1,ibelly=0,
ntt=3, tempi=0.0,temp0=298.0, tautp=0.5, gamma_ln=2.0,
ntp=1, taup=0.5,ig=-1,
ntb=2, ntc=2, ntf=1,
cut=10.0, nsnb=20,dt=0.002,
nstlim=65000,nmropt=1,ntr=1,
ntwe=200, ntwx=200, ntpr=50,
icfe=1, clambda=0.05,
ifsc=1,
&end
&wt type='TEMP0',istep1=0,istep2=5000, value1=0.,
value2=100., &end
&wt type='TEMP0',istep1=5001,istep2=10000, value1=100.,
value2=200., &end
&wt type='TEMP0',istep1=10001,istep2=15000, value1=200.,
value2=298., &end
&wt type='TEMP0',istep1=15001,istep2=65000, value1=298.,
value2=298., &end
&wt type='END' &end
Title one
10.0
RES 1 128
END
Title two
10.0
RES 130 136
END
END

In V1 state, Residue 136 (is a WAT) was removed in the V1.top, but other
atoms are with the same coordinate and the same order to V0.top. Thus, in
ifsc=0 and crgmask/scmask=' ' (because I believe that in V1 state, there
are not atoms appearing.), but the process exited..

My V1 inputfile:

density equilibration
&cntrl
imin=0, irest=0, ntx=1,ibelly=0,
ntt=3, tempi=0.0,temp0=298.0, tautp=0.5, gamma_ln=2.0,
ntp=1, taup=0.5,ig=-1,
ntb=2, ntc=2, ntf=1,
cut=10.0, nsnb=20,dt=0.002,
nstlim=65000,nmropt=1,ntr=1,
ntwe=200, ntwx=200, ntpr=50,
icfe=1, clambda=0.05,
ifsc=1,
&end
&wt type='TEMP0',istep1=0,istep2=5000, value1=0.,
value2=100., &end
&wt type='TEMP0',istep1=5001,istep2=10000, value1=100.,
value2=200., &end
&wt type='TEMP0',istep1=10001,istep2=15000, value1=200.,
value2=298., &end
&wt type='TEMP0',istep1=15001,istep2=65000, value1=298.,
value2=298., &end
&wt type='END' &end
Title one
10.0
RES 1 128
END
Title two
10.0
RES 130 135
END
END

On Tue, Oct 1, 2013 at 8:35 PM, Ƚͦ <rantingjing0445019.gmail.com> wrote:

> Dear Prof. David A Case,
>
> Thank you for your help.
> I have did the cases.
>
>
> On Tue, Oct 1, 2013 at 7:37 PM, David A Case <case.biomaps.rutgers.edu>wrote:
>
>> On Tue, Oct 01, 2013, Ƚͦ wrote:
>> >
>> > Yes, I found the erro in the mdout files.Thanks very much. The progam
>> > worked now.
>> > Now, if the V0 state is a protein-ligand complex with one crystal water
>> > (that is PLW(sol) ), and the V1 is a protein-ligand complex with the
>> water
>> > removed (that is PL(sol) + W(g) ). case one
>> > if the V0 state is a solution water (that is W(sol) ), and the V1 is a
>> gas
>> > water (that is W(g) ). case two
>>
>> These sound like exactly the sort of simulation that is covered in the
>> tutorial. For "case two", you can check your answer against literature
>> values
>> (which depend on the water model you are using). Do that case first to
>> gain
>> confidence that you are doing the correct calculations.
>>
>> ...dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> PhD Ting Ran
>
> CPU(CHINA PHARMACEUTICAL UNIVERSITY)
> Molecular-Design & Drug-Discovery Lab
> Laboratory Building A212
> 639 Longmian Avenue
> Nanjing, 210009
> P.R.China
>

```--
PhD Ting Ran
CPU(CHINA PHARMACEUTICAL UNIVERSITY)
Molecular-Design &  Drug-Discovery Lab
Laboratory Building A212
639 Longmian Avenue
Nanjing, 210009
P.R.China
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Received on Wed Oct 02 2013 - 04:00:04 PDT
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