Hello!
I am trying to generate topology file for a non-standard amino acid. It is
extremely similar to glutamic acid, just an extra CH2 moiety added to the
side chain. The residue name is AAD and has a total charge of -1. I am
following the amber tutorial B5.
Here is the erorr that I am getting from the saveAmberParam command:
The file contained 1 atoms not in residue templates
Since added/missing = extra, there is a high probability
of atoms with 'incorrect' names; you may want to
use addPdbAtomMap to map these names, or change in file
Checking Unit.
ERROR: The unperturbed charge of the unit: -4.960849 is not integral.
WARNING: The unperturbed charge of the unit: -4.960849 is not zero.
FATAL: Atom .R<AAD 25>.A<O 19> does not have a type.
Failed to generate parameters
Parameter file was not saved.
I am not sure why the total charge went up to -5 (and that too a
non-integral value). Plus, the reason it had to create a new O atom is
because for some reason, prepgen removed the O atom in the prepin file.
Any clue on how to fix this? Also, is this the best way to generate
topology file for a non-standard amino acid?
Thanks for the help,
Chitrak.
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Received on Fri Sep 09 2016 - 15:30:02 PDT
