Would like also to specify regarding (1) question is that
when i do visualisation in VMD of my md trajectory and see atom
numbering within it - it's order always differs on i-1 in comparison
to same system seen using txt editior within dumped pdb. Should I
take information from VMD directly in those case?
2015-03-31 13:58 GMT+02:00 James Starlight <jmsstarlight.gmail.com>:
> thanks a lot!
> couple of question:
>
> 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
>
> e.g for residue taken from pdb consisted of all atoms of the system
> ATOM 3691 N TYR X 234 39.544 24.195 43.488 0.00 0.00
> ATOM 3692 H TYR X 234 39.552 24.496 42.524 0.00 0.00
> ATOM 3693 CA TYR X 234 38.410 24.539 44.400 0.00 0.00
> ATOM 3694 HA TYR X 234 38.825 24.800 45.373 0.00 0.00
> ATOM 3695 CB TYR X 234 37.689 25.887 43.967 0.00 0.00
> ATOM 3696 HB2 TYR X 234 38.460 26.656 43.915 0.00 0.00
> ATOM 3697 HB3 TYR X 234 37.269 25.660 42.987 0.00 0.00
> ATOM 3698 CG TYR X 234 36.578 26.367 44.922 0.00 0.00
> ATOM 3699 CD1 TYR X 234 36.766 27.620 45.583 0.00 0.00
> ATOM 3700 HD1 TYR X 234 37.741 28.065 45.452 0.00 0.00
> ATOM 3701 CE1 TYR X 234 35.802 28.171 46.442 0.00 0.00
> ATOM 3702 HE1 TYR X 234 36.043 29.092 46.952 0.00 0.00
> ATOM 3703 CZ TYR X 234 34.588 27.519 46.575 0.00 0.00
> ATOM 3704 OH TYR X 234 33.662 28.116 47.397 0.00 0.00
> ATOM 3705 HH TYR X 234 34.061 28.923 47.732 0.00 0.00
> ATOM 3706 CE2 TYR X 234 34.401 26.303 45.865 0.00 0.00
> ATOM 3707 HE2 TYR X 234 33.407 25.881 45.864 0.00 0.00
> ATOM 3708 CD2 TYR X 234 35.371 25.704 45.042 0.00 0.00
> ATOM 3709 HD2 TYR X 234 35.214 24.832 44.424 0.00 0.00
> ATOM 3710 C TYR X 234 37.308 23.419 44.744 0.00 0.00
> ATOM 3711 O TYR X 234 36.898 23.283 45.890 0.00 0.00
>
> my atoms for Chi-1 should be 3693 (CA) , 3695 (CB), 3698 (CG), 3699 (CD1)
>
> Does the atom numbering after such conversion will be the same as used
> for the amber ? Is it possible to obtain numbering directly from one
> of the amber files avoiding VMD?
>
>
> 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.)
>
> James
>
> 2015-03-30 17:19 GMT+02:00 David A Case <case.biomaps.rutgers.edu>:
>> On Mon, Mar 30, 2015, James Starlight wrote:
>>>
>>> could someone provide with some example of such realization
>>> considering my task (e.g just to restrain CHI-1 side-chain dihedral
>>> angle of specified residue within it range of +80 to +100 degrees)?
>>> I've found only such example in Refinement of a DNA Duplex tutorial
>>> which seems for me allitle tricky :-) Is it possible just to define
>>> all nessesary inputs within md_input.in file using mnropt flag for
>>> instance ?
>>>
>>
>> Be sure to read Section 23.1 of the Reference Manual. You can set nmropt=1
>> and add something like the following to the DISANG file:
>>
>> &wt iat=?,?,?,?, r1=70., r2=80., r3=100., r4=110., rk2=??., rk3=??, /
>>
>> Here the iat's are the atom numbers that identify the torsion you wish to
>> constraint, and the values of rk2 and rk3 depend on how steep a penalty you
>> wish to have when the torsion is outside the allowed value of 80 - 100 deg.
>> You will probably have to run some test simulations to get a idea of what
>> these should be.
>>
>>
>> ....dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 31 2015 - 05:30:05 PDT
