On Sun, Jun 29, 2014 at 9:44 PM, Eugene Yedvabny <eyedvabny.berkeley.edu>
wrote:
> Hello Dr. Roe,
>
> Thank you for the tip! The select @H* command returns the list of atom
> numbers, but I am looking for a more 'physical' label, i.e. "TYR_2.H" as
> is
> used in HBond analysis. Since the select command gives me an atom index, is
> there a command that prints the atom label so I can cross-reference the
> two? If not, I can generate a PDB and extra the labels that way, but I
> first wanted to find out if cpptraj already has this functionality built
> in.
>
When I use cpptraj --mask, I get output that looks like this:
#Atom Name #Res Name #Mol Type Charge Mass GBradius El
2 H1 1 SER 1 H 0.1898 1.0080 1.2000 H
3 H2 1 SER 1 H 0.1898 1.0080 1.2000 H
4 H3 1 SER 1 H 0.1898 1.0080 1.2000 H
6 HA 1 SER 1 HP 0.0782 1.0080 1.2000 H
In this case, use a little awk trickery:
cpptraj -p <prmtop> --mask '.H=' | awk '{printf("%s_%d@%s\n", $4, $3, $2)}'
That should print out something like:
Name_0.Name
SER_1.H1
SER_1.H2
SER_1.H3
SER_1.HA
The first line comes from the comment header and can be deleted. The rest
seems to be the format you want?
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Jun 30 2014 - 07:00:02 PDT
