On Thu, Jan 02, 2025, LI An-Bang via AMBER wrote:
>
>But apparently, script "process_mdout.perl" doesn't deal with the "
>CMAP " line before "Density" line.
>It seems that the " CMAP " line is newly added, but
>"process_mdout.perl" didn't update correspondingly.
Thanks for the report. We will update the process_mdout.perl script
as you suggest.
>
>
>I add the following statements in line 150 of "process_mdout.perl", then it can extract Density data.
>
>
> if (/CMAP/) {
> ($cmap) = /.*CMAP.*=(.*\d*\.\d*)/;
> if ( $debug ) {
> print $_;
> print "cmap is $cmap\n";
> }
> $_ = <INPUT>;
> }
>
>PS. What is the meaning of "EKCMT" and "CMAP"? I searched in
>Amber24.pdf，but didn't found any results about them.
The Amber manual has dozens of references to CMAP, but I agree that it more
or less assumes that readers know what CMAP means. This came originally
from CHARMM, and you can read about it here:
https://charmm-gui.org/?doc=lecture&module=molecules_and_topology&lesson=3
You can also read about this here, in what might be the original publication
(others can correct me if I am wrong):
MacKerell, A. D. 2004. Empirical force fields for biological macromolecules: overview and issues. J. Comput. Chem. 25:1584–1606
We should update the file formats web page and explanations in Chapter 14 in
the Amber Reference Manual to better explain this.
....dac
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Received on Sat Jan 04 2025 - 21:30:03 PST
