[AMBER] process_mdout.perl doesn't extract Density data

From: LI An-Bang via AMBER <amber.ambermd.org>
Date: Thu, 2 Jan 2025 10:21:30 +0800

Hi,


I use process_mdout.perl&nbsp; to extract data from ".out" file of production MD, and found that the&nbsp; Density data was not extracted.


I checked the out file and script "process_mdout.perl", and found that the data is following:


&nbsp;NSTEP =&nbsp; &nbsp; &nbsp;3000&nbsp; &nbsp;TIME(PS) =&nbsp; &nbsp; &nbsp; 26.000&nbsp; TEMP(K) =&nbsp; &nbsp;299.74&nbsp; PRESS =&nbsp; -263.7
&nbsp;Etot&nbsp; &nbsp;=&nbsp; &nbsp; -68993.2902&nbsp; EKtot&nbsp; &nbsp;=&nbsp; &nbsp; &nbsp;13497.2295&nbsp; EPtot&nbsp; &nbsp; &nbsp; =&nbsp; &nbsp; -82490.5197
&nbsp;BOND&nbsp; &nbsp;=&nbsp; &nbsp; &nbsp; &nbsp;174.2087&nbsp; ANGLE&nbsp; &nbsp;=&nbsp; &nbsp; &nbsp; &nbsp;496.3624&nbsp; DIHED&nbsp; &nbsp; &nbsp; =&nbsp; &nbsp; &nbsp; &nbsp;365.6343
&nbsp;1-4 NB =&nbsp; &nbsp; &nbsp; &nbsp;192.5854&nbsp; 1-4 EEL =&nbsp; &nbsp; &nbsp; 1915.3936&nbsp; VDWAALS&nbsp; &nbsp; =&nbsp; &nbsp; &nbsp;14605.5558
&nbsp;EELEC&nbsp; =&nbsp; &nbsp;-100268.5665&nbsp; EHBOND&nbsp; =&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0.0000&nbsp; RESTRAINT&nbsp; =&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0.0000
&nbsp;EKCMT&nbsp; =&nbsp; &nbsp; &nbsp; 6401.9621&nbsp; VIRIAL&nbsp; =&nbsp; &nbsp; &nbsp; 7708.5840&nbsp; VOLUME&nbsp; &nbsp; &nbsp;=&nbsp; &nbsp; 229520.5066
&nbsp;CMAP&nbsp; &nbsp;=&nbsp; &nbsp; &nbsp; &nbsp; 28.3067
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Density&nbsp; &nbsp; =&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0.9847
&nbsp;Ewald error estimate:&nbsp; &nbsp;0.2134E-04
&nbsp;------------------------------------------------------------------------------



But apparently, script&nbsp;"process_mdout.perl" doesn't deal with the " CMAP&nbsp;" line before "Density" line.
It seems that the " CMAP&nbsp;" line is newly added, but "process_mdout.perl" didn't update correspondingly.&nbsp;


I add the following statements in line 150 of "process_mdout.perl", then it can extract Density data.


        &nbsp; &nbsp; if (/CMAP/) {
                ($cmap) = /.*CMAP.*=(.*\d*\.\d*)/;
                if ( $debug ) {
                &nbsp; &nbsp; print $_;
                &nbsp; &nbsp; print "cmap is $cmap\n";
                }
                $_ = <INPUT&gt;;
        &nbsp; &nbsp; }



Please check this.



PS. What is the meaning of "EKCMT" and "CMAP"? I searched in Amber24.pdf，but didn't found any results about them.


Anbang Li

Institute of Biophysics, College of Physical Science and Technology,
 Central China Normal University, China


&nbsp;
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 01 2025 - 18:30:02 PST