- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

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.

... making more adjustments ...

WARNING: Local coordinate 6598 differs from partner coordinate 6589 !

SANDER BOMB in subroutine sc_check_and_adjust

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,

crgmask=':136.O,H1,H2', scmask=':136.O,H1,H2',

&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

V1, I used ifsc=1 and crgmask/scmask=' '. Indeed, I had tried to use

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,

crgmask='', scmask='',

&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
*

*>
*

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.

... making more adjustments ...

WARNING: Local coordinate 6598 differs from partner coordinate 6589 !

SANDER BOMB in subroutine sc_check_and_adjust

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,

crgmask=':136.O,H1,H2', scmask=':136.O,H1,H2',

&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

V1, I used ifsc=1 and crgmask/scmask=' '. Indeed, I had tried to use

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,

crgmask='', scmask='',

&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:

-- PhD Ting Ran CPU(CHINA PHARMACEUTICAL UNIVERSITY) Molecular-Design & Drug-Discovery Lab Laboratory Building A212 639 Longmian Avenue Nanjing, 210009 P.R.China _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Oct 02 2013 - 04:00:04 PDT

Custom Search