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 Sat Feb 16 2019 - 21:00:01 PST
