yes
and what those options from the mdin.in file are do?
&wt
type='DISAVI' istep1=1, istep2=10, value1=0, value2=0.0,
&end
here exactly difference between amber 12 and amber 14: because in the
latter &wt is placed within new disang.rst file in comparison to
amber-12 (which I'm using!)
2015-03-31 14:32 GMT+02:00 David A Case <case.biomaps.rutgers.edu>:
> On Tue, Mar 31, 2015, James Starlight wrote:
>>
>> is it possible to provide some amber mask for defining of the
>> restrained atoms for iat term within DISANG file
>> or alternative I should to dump some pdb from the trajectory using vmd
>> and check it within it
>
> Best to use LEaP or ambpdb to create the PDB file that has the Amber atom
> numbering. What you get from VMD depends on what files you loaded, etc.
>
>>
>> 2) Regarding setup:
>>
>> is it correctly just to provide within my input.in file something like this
>> &cntrl
>> imin=0, ! Molecular dynamics
>> # here all inputs for common simulation are provided
>> nmropt=1,
>> &end
>> &wt
>> type='DISAVI' istep1=1, istep2=10, value1=0, value2=0.0,
>> &end
>> &wt type='END',
>> &end
>> DISANG=disang.rst
>> DUMPAVE=./out/DUMP_PMF
>> END
>> END
>>
>> and with the something like this to the disang.rst :
>>
>> &rst nstep1=1, nstep2=25000000, iat=35,40,190,185,
>> iresid=0, ifvari=0,
>> r1=70.0, r2=85.0, r3=115.0, r4=125.0, rk2=30.0, rk3=30.0,
>> &end
>>
>> so the &wt should be exactly in the first (md input file)? I specify
>> it because I'm using amber-12 for the simulation (not amber-14!) and
>> what I've found in manual
>> : Note that, unlike earlier versions of Amber, the &rst namelists must
>> be in the DISANG file, and not in the mdin file.)
>
> You must make a separate file, and refer to it by the DISANG keyword, as
> mentioned above.
>
> ...dac
>
>
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Received on Tue Mar 31 2015 - 07:30:03 PDT
