Cpptraj uses time as X values for data sets read from mdout. You are using
a 1 fs timestep and writing every 0.5 ps (500 steps). Therefore your final
time value after 24000 steps is 12000 ps. Seems reasonable to me.
-Dan
On Wednesday, March 30, 2016, Sehrish Naz Aijaz <sehrish.naz.outlook.com>
wrote:
> Dear Daniel,
>
> I have tried your readdata script again on my output files and one on my
> friend's output files. we both have same output files. readdata reads and
> lists all 24000 frames but plots only 12000 frames out of those 24000.
> following is the procedure I follow
>
> >cpptraj
>
> CPPTRAJ: Trajectory Analysis. V14.25
>
> ___ ___ ___ ___
>
> | \/ | \/ | \/ |
>
> _|_/\_|_/\_|_/\_|_
>
> > readdata *.out name data
>
> Reading '32a_prod1.out' as Amber MDOUT file with name 'data'
>
> Reading from mdout files: 32a_prod1.out
>
> Processing MDOUT: 32a_prod1.out
>
> 4000 frames
>
> > readdata 32a_prod1.out name data
>
> Reading '32a_prod1.out' as Amber MDOUT file with name 'data'
>
> Reading from mdout files: 32a_prod1.out
>
> Processing MDOUT: 32a_prod1.out
>
> 4000 frames
>
> Warning: Appending to set 'data_Etot'. Using existing X step 0.5
>
> data_Etot: 475.5 <= X <= 4475, 0.5
>
> Warning: Appending to set 'data_EPtot'. Using existing X step 0.5
>
> data_EPtot: 475.5 <= X <= 4475, 0.5
>
> Warning: Appending to set 'data_BOND'. Using existing X step 0.5
>
> data_BOND: 475.5 <= X <= 4475, 0.5
>
> Warning: Appending to set 'data_ANGLE'. Using existing X step 0.5
>
> data_ANGLE: 475.5 <= X <= 4475, 0.5
>
> Warning: Appending to set 'data_DIHED'. Using existing X step 0.5
>
> data_DIHED: 475.5 <= X <= 4475, 0.5
>
> Warning: Appending to set 'data_VDW'. Using existing X step 0.5
>
> data_VDW: 475.5 <= X <= 4475, 0.5
>
> Warning: Appending to set 'data_EELEC'. Using existing X step 0.5
>
> data_EELEC: 475.5 <= X <= 4475, 0.5
>
> Warning: Appending to set 'data_VDW1-4'. Using existing X step 0.5
>
> data_VDW1-4: 475.5 <= X <= 4475, 0.5
>
> Warning: Appending to set 'data_EEL1-4'. Using existing X step 0.5
>
> data_EEL1-4: 475.5 <= X <= 4475, 0.5
>
> Warning: Appending to set 'data_RST'. Using existing X step 0.5
>
> data_RST: 475.5 <= X <= 4475, 0.5
>
> Warning: Appending to set 'data_Density'. Using existing X step 0.5
>
> data_Density: 475.5 <= X <= 4475, 0.5
>
> Warning: Appending to set 'data_EKtot'. Using existing X step 0.5
>
> data_EKtot: 475.5 <= X <= 4475, 0.5
>
> > readdata 32a_prod2.out name data
>
> Reading '32a_prod2.out' as Amber MDOUT file with name 'data'
>
> Reading from mdout files: 32a_prod2.out
>
> Processing MDOUT: 32a_prod2.out
>
> 4000 frames
>
> Warning: Appending to set 'data_Etot'. Using existing X step 0.5
>
> data_Etot: 475.5 <= X <= 6475, 0.5
>
> Warning: Appending to set 'data_EPtot'. Using existing X step 0.5
>
> data_EPtot: 475.5 <= X <= 6475, 0.5
>
> Warning: Appending to set 'data_BOND'. Using existing X step 0.5
>
> data_BOND: 475.5 <= X <= 6475, 0.5
>
> Warning: Appending to set 'data_ANGLE'. Using existing X step 0.5
>
> data_ANGLE: 475.5 <= X <= 6475, 0.5
>
> Warning: Appending to set 'data_DIHED'. Using existing X step 0.5
>
> data_DIHED: 475.5 <= X <= 6475, 0.5
>
> Warning: Appending to set 'data_VDW'. Using existing X step 0.5
>
> data_VDW: 475.5 <= X <= 6475, 0.5
>
> Warning: Appending to set 'data_EELEC'. Using existing X step 0.5
>
> data_EELEC: 475.5 <= X <= 6475, 0.5
>
> Warning: Appending to set 'data_VDW1-4'. Using existing X step 0.5
>
> data_VDW1-4: 475.5 <= X <= 6475, 0.5
>
> Warning: Appending to set 'data_EEL1-4'. Using existing X step 0.5
>
> data_EEL1-4: 475.5 <= X <= 6475, 0.5
>
> Warning: Appending to set 'data_RST'. Using existing X step 0.5
>
> data_RST: 475.5 <= X <= 6475, 0.5
>
> Warning: Appending to set 'data_Density'. Using existing X step 0.5
>
> data_Density: 475.5 <= X <= 6475, 0.5
>
> Warning: Appending to set 'data_EKtot'. Using existing X step 0.5
>
> data_EKtot: 475.5 <= X <= 6475, 0.5
>
> > readdata 32a_prod3.out name data
>
> Reading '32a_prod3.out' as Amber MDOUT file with name 'data'
>
> Reading from mdout files: 32a_prod3.out
>
> Processing MDOUT: 32a_prod3.out
>
> 4000 frames
>
> Warning: Appending to set 'data_Etot'. Using existing X step 0.5
>
> data_Etot: 475.5 <= X <= 8475, 0.5
>
> Warning: Appending to set 'data_EPtot'. Using existing X step 0.5
>
> data_EPtot: 475.5 <= X <= 8475, 0.5
>
> Warning: Appending to set 'data_BOND'. Using existing X step 0.5
>
> data_BOND: 475.5 <= X <= 8475, 0.5
>
> Warning: Appending to set 'data_ANGLE'. Using existing X step 0.5
>
> data_ANGLE: 475.5 <= X <= 8475, 0.5
>
> Warning: Appending to set 'data_DIHED'. Using existing X step 0.5
>
> data_DIHED: 475.5 <= X <= 8475, 0.5
>
> Warning: Appending to set 'data_VDW'. Using existing X step 0.5
>
> data_VDW: 475.5 <= X <= 8475, 0.5
>
> Warning: Appending to set 'data_EELEC'. Using existing X step 0.5
>
> data_EELEC: 475.5 <= X <= 8475, 0.5
>
> Warning: Appending to set 'data_VDW1-4'. Using existing X step 0.5
>
> data_VDW1-4: 475.5 <= X <= 8475, 0.5
>
> Warning: Appending to set 'data_EEL1-4'. Using existing X step 0.5
>
> data_EEL1-4: 475.5 <= X <= 8475, 0.5
>
> Warning: Appending to set 'data_RST'. Using existing X step 0.5
>
> data_RST: 475.5 <= X <= 8475, 0.5
>
> Warning: Appending to set 'data_Density'. Using existing X step 0.5
>
> data_Density: 475.5 <= X <= 8475, 0.5
>
> Warning: Appending to set 'data_EKtot'. Using existing X step 0.5
>
> data_EKtot: 475.5 <= X <= 8475, 0.5
>
> > readdata 32a_prod4.out name data
>
> Reading '32a_prod4.out' as Amber MDOUT file with name 'data'
>
> Reading from mdout files: 32a_prod4.out
>
> Processing MDOUT: 32a_prod4.out
>
> 4000 frames
>
> Warning: Appending to set 'data_Etot'. Using existing X step 0.5
>
> data_Etot: 475.5 <= X <= 10475, 0.5
>
> Warning: Appending to set 'data_EPtot'. Using existing X step 0.5
>
> data_EPtot: 475.5 <= X <= 10475, 0.5
>
> Warning: Appending to set 'data_BOND'. Using existing X step 0.5
>
> data_BOND: 475.5 <= X <= 10475, 0.5
>
> Warning: Appending to set 'data_ANGLE'. Using existing X step 0.5
>
> data_ANGLE: 475.5 <= X <= 10475, 0.5
>
> Warning: Appending to set 'data_DIHED'. Using existing X step 0.5
>
> data_DIHED: 475.5 <= X <= 10475, 0.5
>
> Warning: Appending to set 'data_VDW'. Using existing X step 0.5
>
> data_VDW: 475.5 <= X <= 10475, 0.5
>
> Warning: Appending to set 'data_EELEC'. Using existing X step 0.5
>
> data_EELEC: 475.5 <= X <= 10475, 0.5
>
> Warning: Appending to set 'data_VDW1-4'. Using existing X step 0.5
>
> data_VDW1-4: 475.5 <= X <= 10475, 0.5
>
> Warning: Appending to set 'data_EEL1-4'. Using existing X step 0.5
>
> data_EEL1-4: 475.5 <= X <= 10475, 0.5
>
> Warning: Appending to set 'data_RST'. Using existing X step 0.5
>
> data_RST: 475.5 <= X <= 10475, 0.5
>
> Warning: Appending to set 'data_Density'. Using existing X step 0.5
>
> data_Density: 475.5 <= X <= 10475, 0.5
>
> Warning: Appending to set 'data_EKtot'. Using existing X step 0.5
>
> data_EKtot: 475.5 <= X <= 10475, 0.5
>
> > readdata 32a_prod5.out name data
>
> Reading '32a_prod5.out' as Amber MDOUT file with name 'data'
>
> Reading from mdout files: 32a_prod5.out
>
> Processing MDOUT: 32a_prod5.out
>
> 4000 frames
>
> Warning: Appending to set 'data_Etot'. Using existing X step 0.5
>
> data_Etot: 475.5 <= X <= 12475, 0.5
>
> Warning: Appending to set 'data_EPtot'. Using existing X step 0.5
>
> data_EPtot: 475.5 <= X <= 12475, 0.5
>
> Warning: Appending to set 'data_BOND'. Using existing X step 0.5
>
> data_BOND: 475.5 <= X <= 12475, 0.5
>
> Warning: Appending to set 'data_ANGLE'. Using existing X step 0.5
>
> data_ANGLE: 475.5 <= X <= 12475, 0.5
>
> Warning: Appending to set 'data_DIHED'. Using existing X step 0.5
>
> data_DIHED: 475.5 <= X <= 12475, 0.5
>
> Warning: Appending to set 'data_VDW'. Using existing X step 0.5
>
> data_VDW: 475.5 <= X <= 12475, 0.5
>
> Warning: Appending to set 'data_EELEC'. Using existing X step 0.5
>
> data_EELEC: 475.5 <= X <= 12475, 0.5
>
> Warning: Appending to set 'data_VDW1-4'. Using existing X step 0.5
>
> data_VDW1-4: 475.5 <= X <= 12475, 0.5
>
> Warning: Appending to set 'data_EEL1-4'. Using existing X step 0.5
>
> data_EEL1-4: 475.5 <= X <= 12475, 0.5
>
> Warning: Appending to set 'data_RST'. Using existing X step 0.5
>
> data_RST: 475.5 <= X <= 12475, 0.5
>
> Warning: Appending to set 'data_Density'. Using existing X step 0.5
>
> data_Density: 475.5 <= X <= 12475, 0.5
>
> Warning: Appending to set 'data_EKtot'. Using existing X step 0.5
>
> data_EKtot: 475.5 <= X <= 12475, 0.5
>
> > list dataset
>
>
>
> DATASETS:
>
> 12 data sets:
>
> data[Etot] "data_Etot" (double), size is 24000
>
> data[EPtot] "data_EPtot" (double), size is 24000
>
> data[BOND] "data_BOND" (double), size is 24000
>
> data[ANGLE] "data_ANGLE" (double), size is 24000
>
> data[DIHED] "data_DIHED" (double), size is 24000
>
> data[VDW] "data_VDW" (double), size is 24000
>
> data[EELEC] "data_EELEC" (double), size is 24000
>
> data[VDW1-4] "data_VDW1-4" (double), size is 24000
>
> data[EEL1-4] "data_EEL1-4" (double), size is 24000
>
> data[RST] "data_RST" (double), size is 24000
>
> data[Density] "data_Density" (double), size is 24000
>
> data[EKtot] "data_EKtot" (double), size is 24000
>
> > writedata energy_tot.agr data[Etot]
>
> data_Etot
>
> > writedata energy_full.agr data[*]
>
> data_Etot data_EPtot data_BOND data_ANGLE data_DIHED data_VDW data_EELEC
> data_VDW1-4 data_EEL1-4 data_RST data_Density data_EKtot
>
> > quit
>
> TIME: Total execution time: 132.9724 seconds.
>
>
> --------------------------------------------------------------------------------
>
> I have also attach the picture of my incomplete plot and complete plot of
> my friend's output files. Please guide whats wrong with this while it reads
> all 24000 frames of my output files. Where is the mistake which I am unable
> to understand....
>
>
>
> Regards,
>
> Sehrish Naz
>
> Jr. Research Fellow,
> Computational Chemistry Unit.
> Dr. Panjwani Center for Molecular Medicine and Drug Research,
> International Center for Chemical and Biological Sciences,
> University of Karachi, Karachi-75270.
> E-mail: Sehrish.naz.outlook.com
> <javascript:_e(%7B%7D,'cvml','Sehrish.naz.outlook.com');>
>
>
>
> *From: *Sehrish Naz Aijaz
> <javascript:_e(%7B%7D,'cvml','sehrish.naz.outlook.com');>
> *Sent: *29 March 2016 09:03
> *To: *Daniel Roe <javascript:_e(%7B%7D,'cvml','daniel.r.roe.gmail.com');>;
> AMBER Mailing List <javascript:_e(%7B%7D,'cvml','amber.ambermd.org');>
> *Subject: *Re: [AMBER] problem in plotting total energy graphs by perl
> script
>
>
> Sorry to say but I did not receive any mail from your side that’s why I
> again ask for help...
>
> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
> From: Daniel Roe<mailto:daniel.r.roe.gmail.com
> <javascript:_e(%7B%7D,'cvml','daniel.r.roe.gmail.com');>>
> Sent: 28 March 2016 18:37
> To: Sehrish Naz Aijaz<mailto:sehrish.naz.outlook.com
> <javascript:_e(%7B%7D,'cvml','sehrish.naz.outlook.com');>>; AMBER Mailing
> List<mailto:amber.ambermd.org
> <javascript:_e(%7B%7D,'cvml','amber.ambermd.org');>>
> Subject: Re: [AMBER] problem in plotting total energy graphs by perl script
>
> I responded to you 3 days ago (http://archive.ambermd.org/201603/0505.html
> ).
> Did you not receive my reply?
>
> On Monday, March 28, 2016, Sehrish Naz Aijaz <sehrish.naz.outlook.com
> <javascript:_e(%7B%7D,'cvml','sehrish.naz.outlook.com');>>
> wrote:
>
> > Dear all,
> >
> > Please suggest me I am waiting for some reply I am not getting that error
> > regarding readdata what to do next its not taking my output files I
> > guess....
> >
> >
> >
> > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> > Windows 10
> >
> >
> >
> > *From: *Sehrish Naz Aijaz
> > <javascript:_e(%7B%7D,'cvml','sehrish.naz.outlook.com
> <javascript:_e(%7B%7D,'cvml','sehrish.naz.outlook.com');>');>
> > *Sent: *25 March 2016 16:18
> > *To: *Bill Ross <javascript:_e(%7B%7D,'cvml','ross.cgl.ucsf.edu
> <javascript:_e(%7B%7D,'cvml','ross.cgl.ucsf.edu');>');>; AMBER
> > Mailing List <javascript:_e(%7B%7D,'cvml','amber.ambermd.org
> <javascript:_e(%7B%7D,'cvml','amber.ambermd.org');>');>
> > *Subject: *Re: [AMBER] problem in plotting total energy graphs by perl
> > script
> >
> >
> > Dear Bill,
> > I have tried as you said to try just one output file but again its giving
> > the following error as,
> > writedata enegy.agr 32a_prod5.out
> > Writing sets to enegy.agr, format 'Grace File'
> > Warning: '32a_prod5.out' selects no data sets.
> > Warning: 32a_prod5.out does not correspond to any data sets.
> >
> > Warning: File 'enegy.agr' has no sets containing data.
> >
> > And same error message was shown for the command
> > Writedata energy.agr 32a_prod5.out_*
> >
> > Now what to do next please guide me....
> >
> > Regards,
> > Sehrish
> >
> > Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for
> > Windows 10
> >
> > From: Bill Ross<mailto:ross.cgl.ucsf.edu
> <javascript:_e(%7B%7D,'cvml','ross.cgl.ucsf.edu');>
> > <javascript:_e(%7B%7D,'cvml','ross.cgl.ucsf.edu
> <javascript:_e(%7B%7D,'cvml','ross.cgl.ucsf.edu');>');>>
> > Sent: 25 March 2016 10:41
> > To: AMBER Mailing List<mailto:amber.ambermd.org
> <javascript:_e(%7B%7D,'cvml','amber.ambermd.org');>
> > <javascript:_e(%7B%7D,'cvml','amber.ambermd.org
> <javascript:_e(%7B%7D,'cvml','amber.ambermd.org');>');>>
> > Subject: Re: [AMBER] problem in plotting total energy graphs by perl
> script
> >
> > And
> >
> > > writedata energy.agr 32a_prod5.out_*
> >
> > On 3/24/16 10:39 PM, Bill Ross wrote:
> > > Just for fun, please try
> > >
> > > > writedata
> > >
> > > and
> > >
> > > > writedata energy.agr 32a_prod5.out
> > >
> > > Bill
> > >
> > > On 3/24/16 9:59 PM, Sehrish Naz Aijaz wrote:
> > >> Dear Daniel,
> > >> I try to run readdata commands as you mentioned. In the beginning it
> > was going well as follows,
> > >> CPPTRAJ: Trajectory Analysis. V15.00
> > >> ___ ___ ___ ___
> > >> | \/ | \/ | \/ |
> > >> _|_/\_|_/\_|_/\_|_
> > >>
> > >> | Date/time: 03/25/16 09:52:32
> > >> | Available memory: 550.168 MB
> > >>
> > >> Loading previous history from log 'cpptraj.log'
> > >>> readdata *.out
> > >> Reading '32a_prod1.out' as Amber MDOUT file with name
> > '32a_prod1.out'
> > >> Reading from mdout file: 32a_prod1.out
> > >> 4000 frames
> > >> Reading '32a_prod2.out' as Amber MDOUT file with name
> > '32a_prod2.out'
> > >> Reading from mdout file: 32a_prod2.out
> > >> 4000 frames
> > >> Reading '32a_prod3.out' as Amber MDOUT file with name
> > '32a_prod3.out'
> > >> Reading from mdout file: 32a_prod3.out
> > >> 4000 frames
> > >> Reading '32a_prod4.out' as Amber MDOUT file with name
> > '32a_prod4.out'
> > >> Reading from mdout file: 32a_prod4.out
> > >> 4000 frames
> > >> Reading '32a_prod5.out' as Amber MDOUT file with name
> > '32a_prod5.out'
> > >> Reading from mdout file: 32a_prod5.out
> > >> 4000 frames
> > >>> list dataset
> > >> DATASETS:
> > >> 75 data sets:
> > >> 32a_prod1.out[Etot] "32a_prod1.out_Etot" (double), size is
> > 4000
> > >> 32a_prod1.out[EPtot] "32a_prod1.out_EPtot" (double), size is
> > 4000
> > >> 32a_prod1.out[BOND] "32a_prod1.out_BOND" (double), size is
> > 4000
> > >> 32a_prod1.out[ANGLE] "32a_prod1.out_ANGLE" (double), size is
> > 4000
> > >> 32a_prod1.out[DIHED] "32a_prod1.out_DIHED" (double), size is
> > 4000
> > >> 32a_prod1.out[VDW] "32a_prod1.out_VDW" (double), size is
> 4000
> > >> 32a_prod1.out[EELEC] "32a_prod1.out_EELEC" (double), size is
> > 4000
> > >> 32a_prod1.out[VDW1-4] "32a_prod1.out_VDW1-4" (double), size
> > is 4000
> > >> 32a_prod1.out[EEL1-4] "32a_prod1.out_EEL1-4" (double), size
> > is 4000
> > >> 32a_prod1.out[RST] "32a_prod1.out_RST" (double), size is
> 4000
> > >> 32a_prod1.out[Density] "32a_prod1.out_Density" (double),
> size
> > is 4000
> > >> 32a_prod1.out[EKtot] "32a_prod1.out_EKtot" (double), size is
> > 4000
> > >> 32a_prod1.out[VOLUME] "32a_prod1.out_VOLUME" (double), size
> > is 4000
> > >> 32a_prod1.out[TEMP] "32a_prod1.out_TEMP" (double), size is
> > 4000
> > >> 32a_prod1.out[PRESS] "32a_prod1.out_PRESS" (double), size is
> > 4000
> > >> 32a_prod2.out[Etot] "32a_prod2.out_Etot" (double), size is
> > 4000
> > >> 32a_prod2.out[EPtot] "32a_prod2.out_EPtot" (double), size is
> > 4000
> > >> 32a_prod2.out[BOND] "32a_prod2.out_BOND" (double), size is
> > 4000
> > >> 32a_prod2.out[ANGLE] "32a_prod2.out_ANGLE" (double), size is
> > 4000
> > >> 32a_prod2.out[DIHED] "32a_prod2.out_DIHED" (double), size is
> > 4000
> > >> 32a_prod2.out[VDW] "32a_prod2.out_VDW" (double), size is
> 4000
> > >> 32a_prod2.out[EELEC] "32a_prod2.out_EELEC" (double), size is
> > 4000
> > >> 32a_prod2.out[VDW1-4] "32a_prod2.out_VDW1-4" (double), size
> > is 4000
> > >> 32a_prod2.out[EEL1-4] "32a_prod2.out_EEL1-4" (double), size
> > is 4000
> > >> 32a_prod2.out[RST] "32a_prod2.out_RST" (double), size is
> 4000
> > >> 32a_prod2.out[Density] "32a_prod2.out_Density" (double),
> size
> > is 4000
> > >> 32a_prod2.out[EKtot] "32a_prod2.out_EKtot" (double), size is
> > 4000
> > >> 32a_prod2.out[VOLUME] "32a_prod2.out_VOLUME" (double), size
> > is 4000
> > >> 32a_prod2.out[TEMP] "32a_prod2.out_TEMP" (double), size is
> > 4000
> > >> 32a_prod2.out[PRESS] "32a_prod2.out_PRESS" (double), size is
> > 4000
> > >> 32a_prod3.out[Etot] "32a_prod3.out_Etot" (double), size is
> > 4000
> > >> 32a_prod3.out[EPtot] "32a_prod3.out_EPtot" (double), size is
> > 4000
> > >> 32a_prod3.out[BOND] "32a_prod3.out_BOND" (double), size is
> > 4000
> > >> 32a_prod3.out[ANGLE] "32a_prod3.out_ANGLE" (double), size is
> > 4000
> > >> 32a_prod3.out[DIHED] "32a_prod3.out_DIHED" (double), size is
> > 4000
> > >> 32a_prod3.out[VDW] "32a_prod3.out_VDW" (double), size is
> 4000
> > >> 32a_prod3.out[EELEC] "32a_prod3.out_EELEC" (double), size is
> > 4000
> > >> 32a_prod3.out[VDW1-4] "32a_prod3.out_VDW1-4" (double), size
> > is 4000
> > >> 32a_prod3.out[EEL1-4] "32a_prod3.out_EEL1-4" (double), size
> > is 4000
> > >> 32a_prod3.out[RST] "32a_prod3.out_RST" (double), size is
> 4000
> > >> 32a_prod3.out[Density] "32a_prod3.out_Density" (double),
> size
> > is 4000
> > >> 32a_prod3.out[EKtot] "32a_prod3.out_EKtot" (double), size is
> > 4000
> > >> 32a_prod3.out[VOLUME] "32a_prod3.out_VOLUME" (double), size
> > is 4000
> > >> 32a_prod3.out[TEMP] "32a_prod3.out_TEMP" (double), size is
> > 4000
> > >> 32a_prod3.out[PRESS] "32a_prod3.out_PRESS" (double), size is
> > 4000
> > >> 32a_prod4.out[Etot] "32a_prod4.out_Etot" (double), size is
> > 4000
> > >> 32a_prod4.out[EPtot] "32a_prod4.out_EPtot" (double), size is
> > 4000
> > >> 32a_prod4.out[BOND] "32a_prod4.out_BOND" (double), size is
> > 4000
> > >> 32a_prod4.out[ANGLE] "32a_prod4.out_ANGLE" (double), size is
> > 4000
> > >> 32a_prod4.out[DIHED] "32a_prod4.out_DIHED" (double), size is
> > 4000
> > >> 32a_prod4.out[VDW] "32a_prod4.out_VDW" (double), size is
> 4000
> > >> 32a_prod4.out[EELEC] "32a_prod4.out_EELEC" (double), size is
> > 4000
> > >> 32a_prod4.out[VDW1-4] "32a_prod4.out_VDW1-4" (double), size
> > is 4000
> > >> 32a_prod4.out[EEL1-4] "32a_prod4.out_EEL1-4" (double), size
> > is 4000
> > >> 32a_prod4.out[RST] "32a_prod4.out_RST" (double), size is
> 4000
> > >> 32a_prod4.out[Density] "32a_prod4.out_Density" (double),
> size
> > is 4000
> > >> 32a_prod4.out[EKtot] "32a_prod4.out_EKtot" (double), size is
> > 4000
> > >> 32a_prod4.out[VOLUME] "32a_prod4.out_VOLUME" (double), size
> > is 4000
> > >> 32a_prod4.out[TEMP] "32a_prod4.out_TEMP" (double), size is
> > 4000
> > >> 32a_prod4.out[PRESS] "32a_prod4.out_PRESS" (double), size is
> > 4000
> > >> 32a_prod5.out[Etot] "32a_prod5.out_Etot" (double), size is
> > 4000
> > >> 32a_prod5.out[EPtot] "32a_prod5.out_EPtot" (double), size is
> > 4000
> > >> 32a_prod5.out[BOND] "32a_prod5.out_BOND" (double), size is
> > 4000
> > >> 32a_prod5.out[ANGLE] "32a_prod5.out_ANGLE" (double), size is
> > 4000
> > >> 32a_prod5.out[DIHED] "32a_prod5.out_DIHED" (double), size is
> > 4000
> > >> 32a_prod5.out[VDW] "32a_prod5.out_VDW" (double), size is
> 4000
> > >> 32a_prod5.out[EELEC] "32a_prod5.out_EELEC" (double), size is
> > 4000
> > >> 32a_prod5.out[VDW1-4] "32a_prod5.out_VDW1-4" (double), size
> > is 4000
> > >> 32a_prod5.out[EEL1-4] "32a_prod5.out_EEL1-4" (double), size
> > is 4000
> > >> 32a_prod5.out[RST] "32a_prod5.out_RST" (double), size is
> 4000
> > >> 32a_prod5.out[Density] "32a_prod5.out_Density" (double),
> size
> > is 4000
> > >> 32a_prod5.out[EKtot] "32a_prod5.out_EKtot" (double), size is
> > 4000
> > >> 32a_prod5.out[VOLUME] "32a_prod5.out_VOLUME" (double), size
> > is 4000
> > >> 32a_prod5.out[TEMP] "32a_prod5.out_TEMP" (double), size is
> > 4000
> > >> 32a_prod5.out[PRESS] "32a_prod5.out_PRESS" (double), size is
> > 4000
> > >> but when I type the command;
> > >> writedata energy.agr *.out
> > >> it gave the following error;
> > >> writedata energy.agr *.out
> > >> Writing sets to energy.agr, format 'Grace File'
> > >> Warning: '*.out' selects no data sets.
> > >> Warning: *.out does not correspond to any data sets.
> > >>
> > >> Warning: File 'energy.agr' has no sets containing data.
> > >> where I am doing mistake???
> > >> I try to give all output files in writedata commamd as,
> > >>> writedata energy.agr 32a_prod1.out 32a_prod2.out 32a_prod3.out
> > 32a_prod4.out 32a_prod5.out
> > >> Writing sets to energy.agr, format 'Grace File'
> > >> Warning: '32a_prod1.out' selects no data sets.
> > >> Warning: 32a_prod1.out does not correspond to any data sets.
> > >> Warning: '32a_prod2.out' selects no data sets.
> > >> Warning: 32a_prod2.out does not correspond to any data sets.
> > >> Warning: '32a_prod3.out' selects no data sets.
> > >> Warning: 32a_prod3.out does not correspond to any data sets.
> > >> Warning: '32a_prod4.out' selects no data sets.
> > >> Warning: 32a_prod4.out does not correspond to any data sets.
> > >> Warning: '32a_prod5.out' selects no data sets.
> > >> Warning: 32a_prod5.out does not correspond to any data sets.
> > >>
> > >> Warning: File 'energy.agr' has no sets containing data.
> > >> again getting the same error. Please suggest me where am I doing
> > mistake??
> > >>
> > >>
> > >> Regards,
> > >> Sehrish Naz
> > >>
> > >>
> > >>
> > >> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for
> > Windows 10
> > >>
> > >> From: Daniel Roe<mailto:daniel.r.roe.gmail.com
> <javascript:_e(%7B%7D,'cvml','daniel.r.roe.gmail.com');>
> > <javascript:_e(%7B%7D,'cvml','daniel.r.roe.gmail.com
> <javascript:_e(%7B%7D,'cvml','daniel.r.roe.gmail.com');>');>>
> > >> Sent: 22 March 2016 21:01
> > >> Cc: AMBER Mailing List<mailto:amber.ambermd.org
> <javascript:_e(%7B%7D,'cvml','amber.ambermd.org');>
> > <javascript:_e(%7B%7D,'cvml','amber.ambermd.org
> <javascript:_e(%7B%7D,'cvml','amber.ambermd.org');>');>>
> > >> Subject: Re: [AMBER] problem in plotting total energy graphs by perl
> > script
> > >>
> > >> On Tue, Mar 22, 2016 at 9:50 AM, Sehrish Naz Aijaz
> > >> <sehrish.naz.outlook.com
> <javascript:_e(%7B%7D,'cvml','sehrish.naz.outlook.com');>
> > <javascript:_e(%7B%7D,'cvml','sehrish.naz.outlook.com
> <javascript:_e(%7B%7D,'cvml','sehrish.naz.outlook.com');>');>> wrote:
> > >>> Can you please tell me the command you are suggesting because I have
> > heard
> > >>> this command first time please guide me.
> > >> Assuming you have cpptraj installed you can do it interactively. Here
> > >> is an example.
> > >>
> > >> $ cpptraj
> > >> > readdata md.out
> > >> Reading 'md.out' as Amber MDOUT file with name 'md.out'
> > >> Reading from mdout file: md.out
> > >> 100000 frames
> > >> > list dataset
> > >>
> > >> DATASETS (14 total):
> > >> md.out[Etot] "md.out_Etot" (double), size is 100000
> > >> md.out[EPtot] "md.out_EPtot" (double), size is 100000
> > >> md.out[BOND] "md.out_BOND" (double), size is 100000
> > >> md.out[ANGLE] "md.out_ANGLE" (double), size is 100000
> > >> md.out[DIHED] "md.out_DIHED" (double), size is 100000
> > >> md.out[VDW] "md.out_VDW" (double), size is 100000
> > >> md.out[EELEC] "md.out_EELEC" (double), size is 100000
> > >> md.out[VDW1-4] "md.out_VDW1-4" (double), size is 100000
> > >> md.out[EEL1-4] "md.out_EEL1-4" (double), size is 100000
> > >> md.out[RST] "md.out_RST" (double), size is 100000
> > >> md.out[EAMBER] "md.out_EAMBER" (double), size is 100000
> > >> md.out[EKtot] "md.out_EKtot" (double), size is 100000
> > >> md.out[TEMP] "md.out_TEMP" (double), size is 100000
> > >> md.out[PRESS] "md.out_PRESS" (double), size is 100000
> > >> > writedata energy.agr md.out[*]
> > >> Writing sets to energy.agr, format 'Grace File'
> > >> md.out_Etot md.out_EPtot md.out_BOND md.out_ANGLE md.out_DIHED
> > >> md.out_VDW md.out_EELEC md.out_VDW1-4 md.out_EEL1-4 md.out_RST
> > >> md.out_EAMBER md.out_EKtot md.out_TEMP md.out_PRESS
> > >> > quit
> > >>
> > >> Then the file energy.agr will contain all of your energy data sets. If
> > >> you just wanted e.g. the total potential energy you would use
> > >> 'writedata eptot.agr md.out[EPtot]' instead.
> > >>
> > >> Hope this helps.
> > >>
> > >> -Dan
> > >>
> > >>> Thanks,
> > >>>
> > >>>
> > >>>
> > >>> Sent from Mail for Windows 10
> > >>>
> > >>>
> > >>>
> > >>> From: Daniel Roe
> > >>> Sent: 21 March 2016 19:38
> > >>> To: AMBER Mailing List
> > >>>
> > >>>
> > >>> Subject: Re: [AMBER] problem in plotting total energy graphs by perl
> > script
> > >>>
> > >>>
> > >>>
> > >>> Hi,
> > >>>
> > >>> FYI you can also use cpptraj to extract energies from MDOUT files via
> > >>> the 'readdata' command. You can then analyze the data or write it out
> > >>> into any format supported by cpptraj.
> > >>>
> > >>> -Dan
> > >>>
> > >>>
> > >>> On Sun, Mar 20, 2016 at 10:56 PM, Sehrish Naz Aijaz
> > >>> <sehrish.naz.outlook.com
> <javascript:_e(%7B%7D,'cvml','sehrish.naz.outlook.com');>
> > <javascript:_e(%7B%7D,'cvml','sehrish.naz.outlook.com
> <javascript:_e(%7B%7D,'cvml','sehrish.naz.outlook.com');>');>> wrote:
> > >>>> Dear Bill,
> > >>>> Are you asking about mden content in my output files??? Or you are
> > saying
> > >>>> to use mden file generated during production runs???
> > >>>> Can you tell me how can I plot those mden file which scripts will
> > help for
> > >>>> plotting and processing mden files???
> > >>>>
> > >>>> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for
> > Windows
> > >>>> 10
> > >>>>
> > >>>> From: Bill Ross<mailto:ross.cgl.ucsf.edu
> <javascript:_e(%7B%7D,'cvml','ross.cgl.ucsf.edu');>
> > <javascript:_e(%7B%7D,'cvml','ross.cgl.ucsf.edu
> <javascript:_e(%7B%7D,'cvml','ross.cgl.ucsf.edu');>');>>
> > >>>> Sent: 20 March 2016 01:11
> > >>>> To: AMBER Mailing List<mailto:amber.ambermd.org
> <javascript:_e(%7B%7D,'cvml','amber.ambermd.org');>
> > <javascript:_e(%7B%7D,'cvml','amber.ambermd.org
> <javascript:_e(%7B%7D,'cvml','amber.ambermd.org');>');>>
> > >>>> Subject: Re: [AMBER] problem in plotting total energy graphs by perl
> > >>>> script
> > >>>>
> > >>>> Have you looked at mden file contents? They could be easier to work
> > with.
> > >>>>
> > >>>> Bill
> > >>>>
> > >>>> On 3/19/16 3:16 AM, Sehrish Naz Aijaz wrote:
> > >>>>> Dear Hai,
> > >>>>> I try to run this in my amber12 but it gives the following error.
> > Can you
> > >>>>> explain this to me...
> > >>>>> Traceback (most recent call last):
> > >>>>> File "/usr/local/amber14/bin/mdout_analyzer.py", line 3, in
> > <module>
> > >>>>> from tkFileDialog import askopenfilenames
> > >>>>> ImportError: No module named tkFileDialog
> > >>>>>
> > >>>>> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for
> > >>>>> Windows 10
> > >>>>>
> > >>>>> From: Hai Nguyen<mailto:nhai.qn.gmail.com
> <javascript:_e(%7B%7D,'cvml','nhai.qn.gmail.com');>
> > <javascript:_e(%7B%7D,'cvml','nhai.qn.gmail.com
> <javascript:_e(%7B%7D,'cvml','nhai.qn.gmail.com');>');>>
> > >>>>> Sent: 19 March 2016 14:48
> > >>>>> To: AMBER Mailing List<mailto:amber.ambermd.org
> <javascript:_e(%7B%7D,'cvml','amber.ambermd.org');>
> > <javascript:_e(%7B%7D,'cvml','amber.ambermd.org
> <javascript:_e(%7B%7D,'cvml','amber.ambermd.org');>');>>
> > >>>>> Subject: Re: [AMBER] problem in plotting total energy graphs by
> perl
> > >>>>> script
> > >>>>>
> > >>>>> I think it should be compatible (Jason might correct me if I am
> > wrong).
> > >>>>>
> > >>>>> Here is the tutorial:
> > http://jswails.wikidot.com/helpful-scripts#toc8
> > >>>>>
> > >>>>> Cheers
> > >>>>> Hai
> > >>>>>
> > >>>>> On Sat, Mar 19, 2016 at 2:26 AM, Sehrish Naz Aijaz
> > >>>>> <sehrish.naz.outlook.com
> <javascript:_e(%7B%7D,'cvml','sehrish.naz.outlook.com');>
> > <javascript:_e(%7B%7D,'cvml','sehrish.naz.outlook.com
> <javascript:_e(%7B%7D,'cvml','sehrish.naz.outlook.com');>');>>
> > >>>>> wrote:
> > >>>>>
> > >>>>>> Dear Hai,
> > >>>>>> I have amber12 in my system. Is this script compatible for amber12
> > which
> > >>>>>> I
> > >>>>>> think not compatible with amber12. So what should I do???
> > >>>>>>
> > >>>>>> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986>
> for
> > >>>>>> Windows 10
> > >>>>>>
> > >>>>>> From: Hai Nguyen<mailto:nhai.qn.gmail.com
> <javascript:_e(%7B%7D,'cvml','nhai.qn.gmail.com');>
> > <javascript:_e(%7B%7D,'cvml','nhai.qn.gmail.com
> <javascript:_e(%7B%7D,'cvml','nhai.qn.gmail.com');>');>>
> > >>>>>> Sent: 19 March 2016 13:56
> > >>>>>> To: AMBER Mailing List<mailto:amber.ambermd.org
> <javascript:_e(%7B%7D,'cvml','amber.ambermd.org');>
> > <javascript:_e(%7B%7D,'cvml','amber.ambermd.org
> <javascript:_e(%7B%7D,'cvml','amber.ambermd.org');>');>>
> > >>>>>> Subject: Re: [AMBER] problem in plotting total energy graphs by
> perl
> > >>>>>> script
> > >>>>>>
> > >>>>>> Can you try to use mdout_analyzer.py in AmberTools15? (It's pain
> to
> > >>>>>> debug
> > >>>>>> Perl code)
> > >>>>>>
> > >>>>>> Check http://ambermd.org/doc12/Amber15.pdf (page 515)
> > >>>>>>
> > >>>>>> Hai
> > >>>>>>
> > >>>>>> On Sat, Mar 19, 2016 at 1:25 AM, Sehrish Naz Aijaz <
> > >>>>>> sehrish.naz.outlook.com
> <javascript:_e(%7B%7D,'cvml','sehrish.naz.outlook.com');>
> > <javascript:_e(%7B%7D,'cvml','sehrish.naz.outlook.com
> <javascript:_e(%7B%7D,'cvml','sehrish.naz.outlook.com');>');>>
> > >>>>>> wrote:
> > >>>>>>
> > >>>>>>> Dear all,
> > >>>>>>> I had run 10 ns simulation (AMBER12) of large compounds in TIP3P
> > box
> > >>>>>>> to
> > >>>>>>> check their stable conformation with time. the input file I used
> > for
> > >>>>>>> production is
> > >>>>>>> NPT production with no restrains
> > >>>>>>> &cntrl
> > >>>>>>> imin=0, ntx=7, irest=1, ntrx=1, ntxo=1,
> > >>>>>>> ntpr=500, ntwx=500, ntwv=200, ntwe=200,
> > >>>>>>> ntf=2, ntb=2, cut=10.0,
> > >>>>>>> nsnb=100, igb=0,
> > >>>>>>> nstlim=2000000,
> > >>>>>>> t=0.0, dt=0.001,
> > >>>>>>> ntt=3, gamma_ln=1.0, tempi=300.0, temp0=300.0,
> > >>>>>>> vlimit=20,
> > >>>>>>> ntp=1, taup=1.0, pres0=1.0, comp=44.6,
> > >>>>>>> ntc=2, tol=0.00000001,
> > >>>>>>> /
> > >>>>>>>
> > >>>>>>> after getting the production files. I tried to calculate the
> total
> > >>>>>>> energy
> > >>>>>>> graphs of the system by using perl script as follows
> > >>>>>>> . #!/usr/bin/perl
> > >>>>>>>
> > >>>>>>>
> > >>>>>>> if ($#ARGV < 0) {
> > >>>>>>> print " Incorrect usage...\n";
> > >>>>>>> exit;
> > >>>>>>> }
> > >>>>>>>
> > >>>>>>>
> > >>>>>>> foreach $i ( 0..$#ARGV ) {
> > >>>>>>> $filein = $ARGV[$i];
> > >>>>>>> $checkfile = $filein;
> > >>>>>>> $checkfile =~ s/\.Z//;
> > >>>>>>> if ( $filein ne $checkfile ) {
> > >>>>>>> open(INPUT, "zcat $filein |") ||
> > >>>>>>> die "Cannot open compressed $filein -- $!\n";
> > >>>>>>> } else {
> > >>>>>>> open(INPUT, $filein) || die "Cannot open $filein -- $!\n";
> > >>>>>>> }
> > >>>>>>> print "Processing sander output file ($filein)...\n";
> > >>>>>>> &process_input;
> > >>>>>>> close(INPUT);
> > >>>>>>> }
> > >>>>>>>
> > >>>>>>> print "Starting output...\n";
> > >>>>>>> @sortedkeys = sort by_number keys(%TIME);
> > >>>>>>> .sortedavgkeys = sort by_number keys(%AVG_TIME);
> > >>>>>>>
> > >>>>>>> foreach $i ( TEMP, TSOLUTE, TSOLVENT, PRES, EKCMT, ETOT, EKTOT,
> > EPTOT,
> > >>>>>>> DENSITY, VOLUME, ESCF ) {
> > >>>>>>> print "Outputing summary.$i\n";
> > >>>>>>> open(OUTPUT, "> summary.$i");
> > >>>>>>> %outarray = eval "\%$i";
> > >>>>>>> foreach $j ( @sortedkeys ) {
> > >>>>>>> print OUTPUT "$j ", $outarray{$j}, "\n";
> > >>>>>>> }
> > >>>>>>> close (OUTPUT);
> > >>>>>>>
> > >>>>>>> print "Outputing summary_avg.$i\n";
> > >>>>>>> open(OUTPUT, "> summary_avg.$i");
> > >>>>>>> %outarray = eval "\%AVG_$i";
> > >>>>>>> foreach $j ( @sortedavgkeys ) {
> > >>>>>>> print OUTPUT "$j ", $outarray{$j}, "\n";
> > >>>>>>> }
> > >>>>>>> close (OUTPUT);
> > >>>>>>>
> > >>>>>>> print "Outputing summary_rms.$i\n";
> > >>>>>>> open(OUTPUT, "> summary_rms.$i");
> > >>>>>>> %outarray = eval "\%RMS_$i";
> > >>>>>>> foreach $j ( @sortedavgkeys ) {
> > >>>>>>> print OUTPUT "$j ", $outarray{$j}, "\n";
> > >>>>>>> }
> > >>>>>>> close (OUTPUT);
> > >>>>>>>
> > >>>>>>>
> > >>>>>>> }
> > >>>>>>>
> > >>>>>>>
> > >>>>>>> sub by_number {
> > >>>>>>> if ($a < $b) {
> > >>>>>>> -1;
> > >>>>>>> } elsif ($a == $b) {
> > >>>>>>> 0;
> > >>>>>>> } elsif ($a > $b) {
> > >>>>>>> 1;
> > >>>>>>> }
> > >>>>>>> }
> > >>>>>>>
> > >>>>>>> sub process_input {
> > >>>>>>>
> > >>>>>>> $status = 0;
> > >>>>>>> $debug = 0;
> > >>>>>>> while ( <INPUT> ) {
> > >>>>>>> $string = $_;
> > >>>>>>>
> > >>>>>>> print $_ if ( ! /NB-upda/ && $debug );
> > >>>>>>>
> > >>>>>>> if (/A V E R A G E S/) {
> > >>>>>>> $averages = 1;
> > >>>>>>> ($averages_over) = /.*O V E R.*(\d*).*S T E P S/;
> > >>>>>>> }
> > >>>>>>>
> > >>>>>>> $rms = 1 if (/R M S/);
> > >>>>>>>
> > >>>>>>> if (/NSTEP/) {
> > >>>>>>> ($time, $temp, $pres) =
> > >>>>>>> /NSTEP =.*TIME.* =(.*\d*\.\d*).*TEMP.*
> > =(.*\d*\.\d*).*PRESS =
> > >>>>>>> (.*\d*\.\d*)/;
> > >>>>>>> if ( $debug ) {
> > >>>>>>> print $_;
> > >>>>>>> print "time is $time, temp is $temp, pres is $pres\n";
> > >>>>>>> }
> > >>>>>>> $_ = <INPUT>;
> > >>>>>>>
> > >>>>>>> if (/Etot/) {
> > >>>>>>> ($etot, $ektot, $eptot) =
> > >>>>>>>
> > >>>>>>>
> /Etot.*=(.*\d*\.\d*).*EKtot.*=(.*\d*\.\d*).*EPtot.*=(.*\d*\.\d*)/;
> > >>>>>>> if ( $debug ) {
> > >>>>>>> print $_;
> > >>>>>>> print "Etot is $etot, ektot is $ektot, eptot is
> > $eptot\n";
> > >>>>>>> }
> > >>>>>>> $_ = <INPUT>;
> > >>>>>>> }
> > >>>>>>> if (/BOND.*ANGLE.*DIHED/) {
> > >>>>>>> ($bond, $angle, $dihedral) =
> > >>>>>>>
> > >>>>>>>
> /BOND.*=(.*\d*\.\d*).*ANGLE.*=(.*\d*\.\d*).*DIHED.*=(.*\d*\.\d*)/;
> > >>>>>>> if ( $debug ) {
> > >>>>>>> print $_;
> > >>>>>>> print "bond is $bond, angle is $angle, dihedral is
> > >>>>>>> $dihedral\n";
> > >>>>>>> }
> > >>>>>>> $_ = <INPUT>;
> > >>>>>>> }
> > >>>>>>> if (/1-4 NB/) {
> > >>>>>>> ($nb14, $eel14, $nb) =
> > >>>>>>> /1-4 NB.*=(.*\d*\.\d*).*1-4
> > >>>>>>> EEL.*=(.*\d*\.\d*).*VDWAALS.*=(.*\d*\.\d*)/;
> > >>>>>>> if ( $debug ) {
> > >>>>>>> print $_;
> > >>>>>>> print "nb14 is $nb14, eel14 is $eel14, vdwaals is
> > $nb\n";
> > >>>>>>> }
> > >>>>>>> $_ = <INPUT>;
> > >>>>>>> }
> > >>>>>>> if (/EELEC/) {
> > >>>>>>> ($eel, $ehbond, $constraint) =
> > >>>>>>>
> > >>>>>>>
> > >>>>>>>
> > /EELEC.*=(.*\d*\.\d*).*EHBOND.*=(.*\d*\.\d*).*CONSTRAINT.*=(.*\d*\.\d*)/;
> > >>>>>>> if ( $debug ) {
> > >>>>>>> print $_;
> > >>>>>>> print "eel is $eel, ehbond is $ehbond, constraint
> is
> > >>>>>>> $constraint\n";
> > >>>>>>> }
> > >>>>>>> $_ = <INPUT>;
> > >>>>>>> #
> > >>>>>>> # check to see if EAMBER is in the mdout file
> > (present
> > >>>>>>> when
> > >>>>>>> # NTR=1)
> > >>>>>>> #
> > >>>>>>> if ( /EAMBER/ ) {
> > >>>>>>> $_ = <INPUT>;
> > >>>>>>> }
> > >>>>>>> }
> > >>>>>>> if (/EKCMT/) {
> > >>>>>>> ($ekcmt, $virial, $volume) =
> > >>>>>>>
> > >>>>>>>
> > /EKCMT.*=(.*\d*\.\d*).*VIRIAL.*=(.*\d*\.\d*).*VOLUME.*=(.*\d*\.\d*)/;
> > >>>>>>> if ( $debug ) {
> > >>>>>>> print $_;
> > >>>>>>> print "Ekcmt is $ekcmt, virial is $virial, volume
> is
> > >>>>>>> $volume\n";
> > >>>>>>> }
> > >>>>>>> $_ = <INPUT>;
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 30 2016 - 05:00:04 PDT
