Hi,
You can try using cpptraj to see what atoms are selected by certain
masks. The '-ms <mask>' command line flag will print atom numbers to
stdout, while '--mask <mask>' will print more details. Interactively,
the 'select' and 'atoms' command will do similar things. The GitHub
version also allows this output to be redirected to a file.
So you could use e.g.
cpptraj -p mytopology.parm7 --mask ':1-10'
to see what is selected by ':1-10'.
Hope this helps,
-Dan
On Thu, Feb 23, 2017 at 1:13 PM, Chris Neale <candrewn.gmail.com> wrote:
> Dear Users:
>
> Are there any tools other than ambmask that will give a print out of the
> atoms that are restrained?
>
> I am using a .prmtop that was generated via parmed gromber and I would like
> to double check my restraint selections. My understanding is that although
> gromber gives a .prmtop that works with pmemd that it is not fully
> functional, hence the use of the keyword CTITLE in place of TITLE, so I
> suppose this behaviour is expected, though a workaround would be useful for
> me.
>
> When I try to use the .prmtop from gromber in ambmask, I get the following
> error:
>
> $ ambmask -p top1222000ps.prmtop -c vtop1222000ps.rst -find '1:587'
> | New format PARM file being parsed.
> | Version = 1.000 Date = 02/07/17 Time = 22:17:49
> ERROR: Flag "TITLE" not found in PARM file
>
>
> If I edit the prmtop file to simple change CTITLE to TITLE then I get the
> following error:
>
> $ ambmask -p x.prmtop -c vtop1222000ps.rst -find '1:587'| New format PARM
> file being parsed.
> | Version = 1.000 Date = 02/07/17 Time = 22:17:49
> natom = 182011
> nres = 42886
> STOP error reading natom from inpcrd
>
> The only other thing that I can think of is to simply run some
> high-temperature dynamics and check per-atom RMSF values to identify which
> atoms ended up getting restrained.
>
> Thank you,
> Chris.
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Feb 23 2017 - 12:00:03 PST
