In addition to what Jason said, you may want to check out some of the
basic Amber tutorials:
http://ambermd.org/tutorials/#basic_tut
In particular the intro to MD (B0) and basic analysis (C0).
-Dan
On Wed, Nov 18, 2015 at 7:12 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Nov 18, 2015 at 8:15 AM, mohammad r <mohammad.r0325.yahoo.com>
> wrote:
>
>> Hi Karl,
>>
>> No I received it from my supervisor and I don't know what it means.
>>
>
> I suspect your advisor said/meant "the backbone is a mess", meaning that
> the secondary and tertiary structures are either nonsensical or not
> expected. But that's just a guess. You should be asking your advisor what
> they meant, not us.
>
>
>
>> Is cpptraj analysis tool a good software for checking all bonds, angles
>> and dihedrals.
>>
>
> Sure. But there is no "check all bonds/angles/dihedrals". There is the
> "check" command that looks for overlaps and long bonds. There is also the
> distance, angle, dihedral, and multidihedral commands that will measure
> specific bonds, angles, and dihedrals, but you have to supply the
> distances/angles/dihedrals you want to be calculated.
>
> Excuse me, do you know any source for building pdb file from protein
>> structure?
>>
>
> I don't know what you mean by "protein structure". The protein structure
> is always defined in some kind of file. Many times it's a PDB file. Other
> file formats also exist -- mol2, PDBx/mmCIF, Amber prmtop/inpcrd, CHARMM
> PSF/crd, Gromacs GRO, .... If you do not have a PDB file, you can create
> one using a program that converts between file formats. cpptraj does this,
> as does openbabel.
>
> In general, you need to be MUCH more specific with your questions on this
> list if you want better help.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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 Wed Nov 18 2015 - 07:30:04 PST
