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 Thu Feb 21 2019 - 08:00:03 PST
