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 Mon Feb 18 2019 - 14:00:03 PST
