On Tue, Mar 22, 2016 at 9:50 AM, Sehrish Naz Aijaz
<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> 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>
>> Sent: 20 March 2016 01:11
>> To: AMBER Mailing List<mailto: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>
>>> Sent: 19 March 2016 14:48
>>> To: AMBER Mailing List<mailto: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>
>>> 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>
>>>> Sent: 19 March 2016 13:56
>>>> To: AMBER Mailing List<mailto: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>
>>>> 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";
>>>>> }
>>>>> $_ = <INPUT>;
>>>>> }
>>>>> if (/T_SOLUTE/) {
>>>>> ($tsolute, $tsolvent) =
>>>>> /T_SOLUTE =(.*\d*\.\d*).*T_SOLVENT =(.*\d*\.\d*)/;
>>>>> if ( $debug ) {
>>>>> print $_;
>>>>> print "Temp solute is $tsolute, temp solvent is
>>>>> $tsolvent\n";
>>>>> }
>>>>> $_ = <INPUT>;
>>>>> }
>>>>>
>>>>> if (/Density/) {
>>>>> ($density) = /.*Density.*=(.*\d*\.\d*)/;
>>>>> if ( $debug ) {
>>>>> print $_;
>>>>> print "Density is $density\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";
>>>>> }
>>>>> $_ = <INPUT>;
>>>>> }
>>>>> if (/ESCF/) {
>>>>> ($escf) =
>>>>> /.*ESCF.*=(.*\d*\.\d*)/;
>>>>> if ( $debug ) {
>>>>> print $_;
>>>>> print "ESCF is $escf\n";
>>>>> }
>>>>> $_ = <INPUT>;
>>>>> }
>>>>>
>>>>> # update arrays
>>>>>
>>>>> if ( $averages == 1 ) {
>>>>> $AVG_TIME{$time} = $time;
>>>>> $AVG_TEMP{$time} = $temp;
>>>>> $AVG_PRES{$time} = $pres;
>>>>> $AVG_ETOT{$time} = $etot;
>>>>> $AVG_EKTOT{$time} = $ektot;
>>>>> $AVG_EPTOT{$time} = $eptot;
>>>>> $AVG_BOND{$time} = $bond;
>>>>> $AVG_ANGLE{$time} = $angle;
>>>>> $AVG_DIHEDRAL{$time} = $dihedral;
>>>>> $AVG_NB14{$time} = $nb14;
>>>>> $AVG_EEL14{$time} = $eel14;
>>>>> $AVG_NB{$time} = $nb;
>>>>> $AVG_EEL{$time} = $eel;
>>>>> $AVG_EHBOND{$time} = $ehbond;
>>>>> $AVG_CONSTRAINT{$time} = $constraint;
>>>>> $AVG_EKCMT{$time} = $ekcmt;
>>>>> $AVG_VIRIAL{$time} = $virial;
>>>>> $AVG_VOLUME{$time} = $volume;
>>>>> $AVG_TSOLUTE{$time} = $tsolute;
>>>>> $AVG_TSOLVENT{$time} = $tsolvent;
>>>>> $AVG_DENSITY{$time} = $density;
>>>>> $AVG_ESCF{$time} = $escf;
>>>>> $averages = 0;
>>>>> } elsif ( $rms == 1 ) {
>>>>> $RMS_TIME{$time} = $time;
>>>>> $RMS_TEMP{$time} = $temp;
>>>>> $RMS_PRES{$time} = $pres;
>>>>> $RMS_ETOT{$time} = $etot;
>>>>> $RMS_EKTOT{$time} = $ektot;
>>>>> $RMS_EPTOT{$time} = $eptot;
>>>>> $RMS_BOND{$time} = $bond;
>>>>> $RMS_ANGLE{$time} = $angle;
>>>>> $RMS_DIHEDRAL{$time} = $dihedral;
>>>>> $RMS_NB14{$time} = $nb14;
>>>>> $RMS_EEL14{$time} = $eel14;
>>>>> $RMS_NB{$time} = $nb;
>>>>> $RMS_EEL{$time} = $eel;
>>>>> $RMS_EHBOND{$time} = $ehbond;
>>>>> $RMS_CONSTRAINT{$time} = $constraint;
>>>>> $RMS_EKCMT{$time} = $ekcmt;
>>>>> $RMS_VIRIAL{$time} = $virial;
>>>>> $RMS_VOLUME{$time} = $volume;
>>>>> $RMS_TSOLUTE{$time} = $tsolute;
>>>>> $RMS_TSOLVENT{$time} = $tsolvent;
>>>>> $RMS_DENSITY{$time} = $density;
>>>>> $RMS_ESCF{$time} = $escf;
>>>>>
>>>>> $rms = 0;
>>>>> } else {
>>>>> $TIME{$time} = $time;
>>>>> $TEMP{$time} = $temp;
>>>>> $PRES{$time} = $pres;
>>>>> $ETOT{$time} = $etot;
>>>>> $EKTOT{$time} = $ektot;
>>>>> $EPTOT{$time} = $eptot;
>>>>> $BOND{$time} = $bond;
>>>>> $ANGLE{$time} = $angle;
>>>>> $DIHEDRAL{$time} = $dihedral;
>>>>> $NB14{$time} = $nb14;
>>>>> $EEL14{$time} = $eel14;
>>>>> $NB{$time} = $nb;
>>>>> $EEL{$time} = $eel;
>>>>> $EHBOND{$time} = $ehbond;
>>>>> $CONSTRAINT{$time} = $constraint;
>>>>> $EKCMT{$time} = $ekcmt;
>>>>> $VIRIAL{$time} = $virial;
>>>>> $VOLUME{$time} = $volume;
>>>>> $TSOLUTE{$time} = $tsolute;
>>>>> $TSOLVENT{$time} = $tsolvent;
>>>>> $DENSITY{$time} = $density;
>>>>> $ESCF{$time} = $escf;
>>>>> }
>>>>>
>>>>> }
>>>>> }
>>>>> }
>>>>>
>>>>> But after running this perl script on the output files I got graph
>>>>> displaying half values of output files as attached here. Can anybody
>>>> guide
>>>>> me whats wrong with the perl graph or my input file as my output files
>>>> are
>>>>> printing all values for energy but perl script plot half values???
>>>>>
>>>>>
>>>>>
>>>>> Sent from Mail for Windows 10
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>> _______________________________________________
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>>>>
>>> _______________________________________________
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> _______________________________________________
>>> AMBER mailing list
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>> _______________________________________________
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>
>
>
> --
> -------------------------
> 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
--
-------------------------
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)
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Received on Tue Mar 22 2016 - 09:30:03 PDT
