Thanks for your answer Daniel. I will try these commands too.
Daniel Roe <daniel.r.roe.gmail.com>, 21 Şub 2019 Per, 18:43 tarihinde şunu
yazdı:
> Hi,
>
> You may want to try the 'makestructure' command in cpptraj, which
> allows you to assign either pre-defined or user-defined backbone
> dihedral angles to specified parts of an input structure. There is
> also the 'rotatedihedral' command, which is a bit more intuitive than
> 'impose' from tleap (in my opinion, but of course I'm biased).
>
> -Dan
>
> On Sat, Feb 16, 2019 at 11:55 PM Erdem Yeler <erdemyeler.gmail.com> wrote:
> >
> > Hi all,
> > I have 2 questions:
> > 1) I am trying to use paramfit to fit my dihedral parameters. My molecule
> > has only 19 atoms and it is monomer already. gen_conformers.sh I should
> > change these lines for my molecule:
> >
> > impose a {2 3}, { {"C" "N" "CA" "C" ${phi}} }
> > impose a {1 2}, { {"C" "N" "CA" "C" ${phi2}} }
> > impose a {2 3}, { {"N" "C" "CA" "N" ${psi}} }
> > impose a {3 4}, { {"N" "C" "CA" "N" ${psi}} }
> >
> > usage is:
> > impose unit seqlist internals
> >
> > in these lines {2 3} are the list of residues. But for a monomer
> molecule I
> > couldn't understand what values to put. is it OK if I put {1 1} seq_list
> > for all dihedrals? For example
> >
> > impose a {1 1}, { {"H" "O" "B" "O" ${psi}} }
> > impose a {1 1}, { {"H" "O" "B" "O" ${psi}} }
> > impose a {1 1}, { {"B" "O" "C" "C" ${psi}} }
> > impose a {1 1}, { {"H" "O" "B" "O" ${psi}} }
> > exc..?
> >
> > 2) When I change this line in gen_conformes.sh for boron atom:
> > from this: addatomtypes { { "oc" "O" "sp3" } }
> > to this: addatomtypes { { "B" "B" "sp2" } }
> > I get this error message in xleap:
> >
> > addAtomTypes: Improper number of arguments!
> > usage: addAtomTypes <list_of_lists>
> >
> > According to gen_conformes.sh the usage seems correct but I couldn't find
> > my mistake.
> > Thank you.
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Received on Fri Feb 22 2019 - 03:00:03 PST
