Hi Amber users,
I'm somewhat new to Amber, and I've been working on getting a working .pdb
file for sulfur dioxide to be used with the ff14SB force field. However,
when I try to load the .pdb file into tleap, I receive an error message
stating that I have duplicate oxygen atoms in my .pdb. I have tried
re-labeling them "O1" and "O2", but that has not fixed the issue. Is there
a way to approach this issue? Thank you for your help.
Here is the tleap output:
Loading PDB file: ./SO2.pdb
-- residue 1: duplicate [O] atoms (total 2)
Warning: Atom names in each residue should be unique.
(Same-name atoms are handled by using the first
occurrence and by ignoring the rest.
Frequently duplicate atom names stem from alternate
conformations in the PDB file.)
Added missing heavy atom: .R<C:\Users\mxw46137\Desktop\SO2al 1>.A<O 2>
total atoms in file: 3
Leap added 1 missing atom according to residue templates:
1 Heavy
Loading parameters: /opt/amber14/dat/leap/parm/frcmod.tip3pf
Reading force field modification type file (frcmod)
Reading title:
This is TIP3P (model F) of Price and Brooks, JCP 121:10096, 2004
(using default radius 1.500000 for O)
(using default radius 1.500000 for O)
(using default radius 1.500000 for S)
Solute vdw bounding box: 4.138 4.485 4.358
Total bounding box for atom centers: 34.138 34.485 34.358
Solvent unit box: 18.774 18.774 18.774
(using default radius 1.500000 for O)
(using default radius 1.500000 for O)
(using default radius 1.500000 for S)
Total vdw box size: 37.182 37.845 37.500 angstroms.
Volume: 52767.387 A^3
Mass > 21709.280 amu, Density > 0.683 g/cc
(type - hence mass - of one or more atoms could not be found)
Added 1205 residues.
removing previous box..
Box dimensions: 34.010417 34.408748 34.118789
Checking Unit.
Building topology.
Building atom parameters.
For atom: .R<C:\Users\mxw46137\Desktop\SO2al 1>.A<S 1> Could not find vdW
(or other) parameters for type: S.3
For atom: .R<C:\Users\mxw46137\Desktop\SO2al 1>.A<O 2> Could not find vdW
(or other) parameters for type: O.2
For atom: .R<C:\Users\mxw46137\Desktop\SO2al 1>.A<O 3> Could not find vdW
(or other) parameters for type: O.2
Parameter file was not saved.
The .pdb file:
ATOM 1 S SO2 1 -0.484 0.000 0.000 1.00 1.5000 S
ATOM 2 O SO2 1 0.485 0.000 -1.156 1.00 1.5000 O
ATOM 3 O SO2 1 0.485 0.000 1.156 1.00 1.5000 O
END
CONECT 1 2 3
CONECT 2 1
CONECT 3 1
Thank you,
Maxwell
--
*Maxwell Conte*
maxwell.conte190.topper.wku.edu
maxwell.conte.gmail.com
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Received on Thu Feb 22 2018 - 09:00:02 PST
