Dear Daniel:
this works (see below). Thank you very much for your help.
cpptraj -p top1222000ps.prmtop --mask ':1-10'
#Atom Name #Res Name #Mol Type Charge Mass GBradius El rVDW
eVDW
1 N 1 MET 1 NH3 -0.3000 7.9590 1.5500 N 1.8500
0.2000
2 H1 1 MET 1 HC 0.3300 3.0240 1.3000 H 0.2245
0.0460
3 H2 1 MET 1 HC 0.3300 3.0240 1.3000 H 0.2245
0.0460
...
On Thu, Feb 23, 2017 at 12:38 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Feb 23 2017 - 12:30:02 PST
