Dear Robin,
thank you for your answer. I will try another software to obtain
conformers.
Robin Betz <robin.robinbetz.com>, 19 Şub 2019 Sal, 00:52 tarihinde şunu
yazdı:
> Hi Erdem,
>
> Your syntax for the impose and addatomtypes commands looks correct, so I'm
> not sure why tleap is giving you an error.
> Are you running Windows? If so, are Windows line endings present in
> gen_conformers.sh? This could be throwing off the parser.
>
> You're correct that with the impose command on only one residue, the
> _seqllist_ argument should only contain 1:
> impose a {1}, {"H" "O" "B" "O" ${psi}} }
>
> In tleap you can run "help impose" for a full description of all of the
> arguments.
>
> There are lots of ways to generate conformers for use with paramfit --
> gen.conformers.sh is just one of them. If it's easier to accomplish this
> in
> a program you're more familiar with I'd probably recommend doing that
> rather than messing with tleap syntax.
>
> Hope this helps,
> Robin
>
> On Sat, Feb 16, 2019 at 8:55 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 Tue Feb 19 2019 - 02:00:02 PST
