On Tue, 2014-08-26 at 18:58 +0100, George Green wrote:
> Just to clarify:
>
> 1) I ran a simulation of a ligand entering a protein binding pocket.
>
> 2) I needed to strip out frames ~0.4A apart as input starting structures
> for different umbrella sampling windows.
I'm confused what exactly you mean here. We usually use "strip" to mean
remove atoms from a system (like stripping waters with the "strip"
command in cpptraj or ParmEd). I think you mean that you need to
extract certain frames (but not strip out any atoms), yes?
> 3) Initially I was attempting to use cpptraj to try and put the box in.
> However, I realised that Jason has a helpful script called
> get_restarts.py that outputs restart files from the initial trajectory. I
> opted to use this and manually modified the box information on the last
> line to match that of the parameter file used in step1.
I'm confused as to how the box was lost in the first place? Just a
little FYI, I wrote get_restarts.py specifically because cpptraj ignored
velocities if they happened to be present in the trajectory file (if you
set ntwv = -1, for instance). But cpptraj does keep track of velocities
now (I'm pretty sure, at least). So the only advantage to using
get_restarts.py is that it's arguably simpler to use (much like a brick
is easier to use than a smartphone).
Or is the box not lost, but you are changing the box to match what the
prmtop file has in it? And if so, why? tleap creates periodic boxes
that are much too large, so I can't really imagine a situation where you
would want to replace a box inside a coordinate file with a box from the
prmtop (not even sander or pmemd use the box info in the prmtop
anymore).
>
> 4) However, now I have a problem during minimisation which tends to stall
> and quit for some of the restart files that form the basis of the various
> US windows. I am currently trying to employ a more gentle two step
> minimisation to try and avoid the minimiser stopping:
>
> ####################
> step1 minimisation - hold all atoms with weak force
> &cntrl
> imin=1, ntmin=1, maxcyc=350, ncyc=200,
> ntb=1, ntpr=5, ntwr=100000, drms=0.05,
> cut=12.0, ntxo=2, ioutfm=1, NTR=1,
> ntc=1, ntf=1,
> ntb=1, ntp=0,
> &end
> Group input for restrained atoms
> 0.5
> RES 1 8866
> END
> END
> ###################
What's the point of this step? These structures come from an MD
simulation, right? So the structure shouldn't be strained, which makes
me think this step isn't doing anything.
>
> Then:
>
> ####################
> step2 minimisation - unrestrained min
> &cntrl
> imin=1, ntmin=1, maxcyc=350, ncyc=200,
> ntb=1, ntpr=5, ntwr=100000, drms=0.05,
> cut=12.0, ntxo=2, ioutfm=1,
> ntc=1, ntf=1,
> ntb=1, ntp=0,
> &end
> &wt
> type='END',
> &end
> DISANG=restraint_list_${frame}.dist
> ###################
>
>
> I'm hoping that you might have some suggestions regarding a better
> minimsation protocol, or alternatively a better way to create the inpcrds
> for umbrella sampling?
I would suggest leaving the box information alone (unless I'm really
missing what you're trying to do).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Aug 26 2014 - 12:30:02 PDT
