Hi, thanks for the response. Initially there is no potassium ion in the pdb.I tried the script as not to add 2 potassium atom specifically and it works well to later neutralize the system.However, if I try back to add initially 2 potassium atom at certain place, first, it added potassium ion as a residue but rename the atom to KFor example here is the pdb map
ATOM 1164 K+ K+ 37 -0.900 4.645 -12.032 1.00 0.00 K
ATOM 1165 K+ K+ 38 -2.581 2.404 -10.169 1.00 0.00 K
ENDCreated a new atom named: K+ within residue: .R<K 37>
Added missing heavy atom: .R<K 37>.A<K 1>
Created a new atom named: K+ within residue: .R<K 38>
Added missing heavy atom: .R<K 38>.A<K 1>
However in the subsequent process, it add the + sign automatically.
FATAL: Atom .R<K 37>.A<K+ 2> does not have a type.FATAL: Atom .R<K 38>.A<K+ 2> does not have a type.
I tried to manually change the pdbatom map to K+ but still the same problem occured.
Yoanes
Pada Rabu, 25 Maret 2020 22.11.09 GMT+1, Thomas Cheatham <tec3.utah.edu> menulis:
> Dear all Amber users,I planned to do simulation of DNA in water. The DNA
> length is 36 bp. However after addition of 2 potassium ion, the input
> file (.inpcrd) was not generated.I get error message from the log
> > saveamberparm wat1 ../input_wat/wat01.prmtop ../input_wat/wat01.inpcrd
>
> Checking Unit.
> FATAL: Atom .R<K 37>.A<K+ 2> does not have a type.
> FATAL: Atom .R<K 38>.A<K+ 2> does not have a type.
The residue name is K which is not consistent with the libraries (assuming
you did load up some ion parameters) so if ion is in the PDB file, change
the residue name to K+.
--tec3_______________________________________________
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Received on Wed Mar 25 2020 - 15:00:01 PDT
