Date: Thu, 16 Apr 2020 00:26:08 +0300
Dear David,
I tried to run here is my input file:
&files
-p x.prmtop
-c x.inpcrd
-o x.out
&end
&configs
% Backbone phi and psi sampling
GridSample :7.O :1.B :6.O :8.C { -180.0 180.0 } fbhw 10.0 Krst
64.0,
% General minimization instructions
count = 64,
verbose 1,
maxcyc = 5000,
strainlim = 20.0,
bstrain = 10.0,
astrain = 10.0,
% Reshuffling conformations to best achieve each minimum
nshuffle = 2,
shuffle bootstrap,
% Output controls
outbase 'Conf', 'Conf',
write 'cdf', 'pdb',
outsuff 'cdf', 'pdb',
&end
and I attached my prmtop and crd files.
But I got this error:
SeekManipulator >> Error. Manipulator command contains too many atom names:
ridSample :7.O :1.B :6.O :8.C { -180.0 180.0 } fbhw 10.0 Krst 64.0
I am very new using mdgx. Could you help me? Where is my mistake?
I want to scan O-B-O-C dihedral from -180 to 180
Thank you.
[image: image.png]
Erdem Yeler <erdemyeler.gmail.com>, 13 Nis 2020 Pzt, 14:37 tarihinde şunu
yazdı:
> Thank you sooo much Dave. I am testing right now :)
>
> David Cerutti <dscerutti.gmail.com>, 13 Nis 2020 Pzt, 09:20 tarihinde
> şunu yazdı:
>
>> Absolutely you can use it for angle and bond scans. Enter three ambmask
>> atom names for angles and specify the range in degrees. For bonds, enter
>> two ambmasks and specify the range in Angstroms.
>>
>> Good luck,
>> Dave
>>
>>
>> On Sun, Apr 12, 2020 at 12:35 AM Erdem Yeler <erdemyeler.gmail.com>
>> wrote:
>>
>> > Dear David,
>> > can we use this for scanning angles and bonds too? Thank you
>> > Dear Elif,
>> > I used paramfit for MM scan but when PES scan has a problem for
>> > non-standart atoms, paramfit reflects this. ;For example: I obtained
>> mol2
>> > files from problematic PES scan. I did this because tleap's impose
>> command
>> > didn't run for boron atoms so I had to obtain different dihedral angles
>> via
>> > PES scan.. and because of the some structure are wrong I saw "a jump"
>> in MM
>> > scan which should not be there.
>> > Erdoniko
>> >
>> > David Cerutti <dscerutti.gmail.com>, 11 Nis 2020 Cmt, 13:53 tarihinde
>> şunu
>> > yazdı:
>> >
>> > > The mdgx program will do what you want: see this tutorial on
>> > conformational
>> > > searching:
>> > >
>> > > http://ambermd.org/tutorials/basic/tutorial6/index.php
>> > >
>> > > Pretty much all you'll need is a topology, a starting coordinates
>> file,
>> > and
>> > > a simple input file where you give it the atom names in ambmasks (i.e.
>> > > :1.CA,
>> > > or :2.OG). It will infer what type of restraint you want based on
>> how
>> > > many
>> > > atoms you tell it are part of the restraint (two for bonds, three for
>> > angle
>> > > restraints, etc.).
>> > >
>> > > It can provide regular or randomized sampling over a specified
>> interval.
>> > > The conformation sampling feeds into force field development
>> protocols:
>> > >
>> > > http://ambermd.org/tutorials/advanced/tutorial32/index.php
>> > >
>> > > Dave
>> > >
>> > >
>> > > On Fri, Apr 10, 2020 at 9:31 PM Elif Çiğdem Calvin <
>> > elifcigdem82.gmail.com
>> > > >
>> > > wrote:
>> > >
>> > > > Hello,
>> > > > in paramfit tutuorial, dihedral angles are changing randomly with an
>> > *.sh
>> > > > file then single point energy calculation performes via this angles
>> (
>> > > Imean
>> > > > structures).
>> > > > I wonder what if I change dihedral angles regularly (for example 5
>> > degree
>> > > > step : 5-10-15-20 ...180 exc..) and then I calculate single point
>> > > energies
>> > > > and I prepare quantum_a.dat file with this data; can I obtain MM
>> scan
>> > in
>> > > > the fit_output_energy.dat as (AMber +K) value? or is it wrong to use
>> > this
>> > > > way to calculate MM scan for a dihedral?
>> > > > _______________________________________________
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>> > > > AMBER.ambermd.org
>> > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > >
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>> > >
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(image/png attachment: image.png)
- application/octet-stream attachment: x.inpcrd
- application/octet-stream attachment: x.prmtop
