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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Received on Thu Feb 23 2017 - 10:30:02 PST
