Hi,
On Tue, Aug 26, 2014 at 11:58 AM, George Green <soyo.green.gmail.com> wrote:
> 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
Out of curiosity, why couldn't you use cpptraj for this? If there is
box info in the input trajectory that box info will be in the output
restart file (as long as 'nobox' is not specified to 'trajout').
-Dan
> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Aug 26 2014 - 12:00:03 PDT
