[AMBER] Creating gaff-suitable PDB file for SO2

From: M Conte <maxwell.conte.gmail.com>
Date: Thu, 1 Mar 2018 00:24:30 -0600

Hi Amber Users,
I'm trying to modify a SO2 .pdb file from the PDB database such that it can
be used in a simulation with GAFF. When I run LeAP, the .prmtop and .inpcrd
files don't generate, and I think that's because of incompatible atom types
or unknown ligand type, but I'm not sure how to correct the situation. Is
it possible to define a new ligand, or would this fit into an existing one?
Thank you in advance for your help.

*PDB file*

ATOM 1 S SO2 1 4.853 -7.956 1.549 1.00 1.5000 s6
ATOM 2 O1 SO2 1 3.488 -7.383 1.304 1.00 1.5000 o
ATOM 3 O2 SO2 1 5.870 -6.854 1.535 1.00 1.5000 o
CONECT 1 2 3

*LEaP output*

Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./tleapScript2.tls
----- Source: /opt/amber14/dat/leap/cmd/leaprc.gaff
----- Source of /opt/amber14/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /opt/amber14/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.7, Nov 2013)
Loading PDB file: ./SO2.pdb
Unknown residue: SO2 number: 0 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
Creating new UNIT for residue: SO2 sequence: 1
Created a new atom named: S within residue: .R<SO2 1>
Created a new atom named: O1 within residue: .R<SO2 1>
Created a new atom named: O2 within residue: .R<SO2 1>
  total atoms in file: 3
  The file contained 3 atoms not in residue templates
solvateBox: Argument #2 is type String must be of type: [unit]
usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]
Box dimensions: 2.382000 1.102000 0.245000
Checking Unit.
FATAL: Atom .R<SO2 1>.A<S 1> does not have a type.
FATAL: Atom .R<SO2 1>.A<O1 2> does not have a type.
FATAL: Atom .R<SO2 1>.A<O2 3> does not have a type.
Failed to generate parameters
Parameter file was not saved.

source leaprc.gaff
SOLSO2 = loadpdb SO2.pdb
solvatebox SOLSO2 TIP3PBOX 15
setbox SOLSO2 centers
saveAmberParm SOLSO2 SO2.prmtop SO2.inpcrd



*Maxwell Conte*
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Received on Wed Feb 28 2018 - 22:30:02 PST
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