[AMBER] Problems adding molecule on Metal-Water system

From: Lucas Bandeira <bandeiralucas97.gmail.com>
Date: Fri, 6 Dec 2019 17:22:44 -0200

Dear AMBER Community,

I'm trying to add a glycerol molecule in my metal-water system, but I get
the following message on my terminal:

GetPDB >> Found 5178 atoms in interfaceNaOH.pdb.
GetPDB >> Bracketed 2708 residues.

GetPDB >> Found 13 atoms in NaOHGlycerol/AmberGlyceroxide.pdb.
GetPDB >> Bracketed 1 residues.

AddToBox >> Examining residue 0
AddToBox >> Added 0 residues.

I've analyzed the pdf file and all the spacing is OK. I'm sending the file
in attachment so you can verify it.

The command I'm using is:

 AddToBox -c interfaceNaOH.pdb -a NaOHGlycerol/AmberGlyceroxide.pdb -na 10
-P 5178 -o interfaceGlycerol.pdb -RW 2.5 -RP 2.5 -G 0.1 -V

Hope you can help me,

Lucas Bandeira
AMBER mailing list
Received on Fri Dec 06 2019 - 11:30:02 PST
Custom Search