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.
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.
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
###################
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?
Many thanks.
On Fri, Aug 22, 2014 at 6:54 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Fri, Aug 22, 2014, George Green wrote:
> >
> > Thanks for pointing that out. I changed the script to the following and
> it
> > now seems to work at the equilibration stage.
> >
> > ###############
> > source leaprc.gaff
> > source leaprc.ff99SBnmr
> > loadAmberParams frcmod.tip4pew
> > loadoff doc_final.lib
> > mol = loadpdb frame5_tryUS.pdb
> > charge mol
> > setBox vdw mol centers
>
> I doubt that this is what you really want. If you know the "correct" box
> sizes, use the "set <unit> box ...." command.
>
> Apologies if I am not really understanding your workflow.
>
> ...regards...dac
>
>
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Received on Tue Aug 26 2014 - 11:00:03 PDT
