Hi Dave - Thanks!
Sorry, I probably wrote that in a confusing way. With sustiva.mol2, if
using antechamber -at gaff2, antechamber and parmchk2 work, but tleap
produces a lot of errors. It seems to also produce output files; I can't
tell if they are correct - I guess I was just worried about the errors.
Without -at gaff2, tleap works without errors, but - according to what
you're saying it would use some kind of inconsistent mix of gaff1 and gaff2
in this case. The log from a full run is copied below.
Best,
Alex
$ antechamber -i sustiva.mol2 -fi mol2 -o lig.mol2 -fo mol2 -c bcc -s 2 -rn
LIG -at gaff2
Welcome to antechamber 20.0: molecular input file processor.
acdoctor mode is on: check and diagnose problems in the input file.
-- Check Format for mol2 File --
Status: pass
Info: Finished reading file (sustiva.mol2); atoms read (30), bonds read
(32).
Info: Determining atomic numbers from atomic symbols which are case
sensitive.
-- Check Unusual Elements --
Status: pass
-- Check Open Valences --
Status: pass
-- Check Geometry --
for those bonded
for those not bonded
Status: pass
-- Check Weird Bonds --
Status: pass
-- Check Number of Units --
Status: pass
acdoctor mode has completed checking the input file.
Running: /home/alex/anaconda3/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
/bin/bash: /home/alex/anaconda3/lib/libtinfo.so.6: no version information
available (required by /bin/bash)
Running: /home/alex/anaconda3/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff2
/bin/bash: /home/alex/anaconda3/lib/libtinfo.so.6: no version information
available (required by /bin/bash)
Info: Total number of electrons: 160; net charge: 0
Running: /home/alex/anaconda3/bin/sqm -O -i sqm.in -o sqm.out
Running: /home/alex/anaconda3/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o
ANTECHAMBER_AM1BCC.AC -f ac -p
/home/alex/anaconda3/dat/antechamber/BCCPARM.DAT -s 2 -j 1
/bin/bash: /home/alex/anaconda3/lib/libtinfo.so.6: no version information
available (required by /bin/bash)
Running: /home/alex/anaconda3/bin/atomtype -f ac -p bcc -o
ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC
/bin/bash: /home/alex/anaconda3/lib/libtinfo.so.6: no version information
available (required by /bin/bash)
$ parmchk2 -i lig.mol2 -f mol2 -o lig.frcmod -s gaff2
$ tleap -f tleap.in
-I: Adding /home/alex/anaconda3/dat/leap/prep to search path.
-I: Adding /home/alex/anaconda3/dat/leap/lib to search path.
-I: Adding /home/alex/anaconda3/dat/leap/parm to search path.
-I: Adding /home/alex/anaconda3/dat/leap/cmd to search path.
-f: Source tleap.in.
Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./tleap.in
----- Source: /home/alex/anaconda3/dat/leap/cmd/leaprc.protein.ff14SB
----- Source of /home/alex/anaconda3/dat/leap/cmd/leaprc.protein.ff14SB done
Log file: ./leap.log
Loading parameters: /home/alex/anaconda3/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /home/alex/anaconda3/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /home/alex/anaconda3/dat/leap/lib/amino12.lib
Loading library: /home/alex/anaconda3/dat/leap/lib/aminoct12.lib
Loading library: /home/alex/anaconda3/dat/leap/lib/aminont12.lib
----- Source: /home/alex/anaconda3/dat/leap/cmd/leaprc.water.tip3p
----- Source of /home/alex/anaconda3/dat/leap/cmd/leaprc.water.tip3p done
Loading library: /home/alex/anaconda3/dat/leap/lib/atomic_ions.lib
Loading library: /home/alex/anaconda3/dat/leap/lib/solvents.lib
Loading parameters: /home/alex/anaconda3/dat/leap/parm/frcmod.tip3p
Reading force field modification type file (frcmod)
Reading title:
This is the additional/replacement parameter set for TIP3P water
Loading parameters:
/home/alex/anaconda3/dat/leap/parm/frcmod.ions1lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6
normal usage set)
Loading parameters: /home/alex/anaconda3/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham
JPCB (2008)
Loading parameters:
/home/alex/anaconda3/dat/leap/parm/frcmod.ions234lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water
model (12-6 normal usage set)
----- Source: /home/alex/anaconda3/dat/leap/cmd/leaprc.gaff2
----- Source of /home/alex/anaconda3/dat/leap/cmd/leaprc.gaff2 done
Log file: ./leap.log
Loading parameters: /home/alex/anaconda3/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
Loading Mol2 file: ./lig.mol2
Reading MOLECULE named LIG
Checking 'LIG'....
Checking parameters for unit 'LIG'.
Checking for bond parameters.
/home/alex/anaconda3/bin/teLeap: Error!
Could not find bond parameter for: ns - ca
/home/alex/anaconda3/bin/teLeap: Error!
Could not find bond parameter for: ns - c
/home/alex/anaconda3/bin/teLeap: Error!
Could not find bond parameter for: ns - hn
Checking for angle parameters.
/home/alex/anaconda3/bin/teLeap: Error!
Could not find angle parameter: o - c - ns
/home/alex/anaconda3/bin/teLeap: Error!
Could not find angle parameter: os - c - ns
/home/alex/anaconda3/bin/teLeap: Error!
Could not find angle parameter: ns - ca - ca
/home/alex/anaconda3/bin/teLeap: Error!
Could not find angle parameter: ns - ca - ca
/home/alex/anaconda3/bin/teLeap: Error!
Could not find angle parameter: ca - ns - c
/home/alex/anaconda3/bin/teLeap: Error!
Could not find angle parameter: ca - ns - hn
/home/alex/anaconda3/bin/teLeap: Error!
Could not find angle parameter: c - ns - hn
/home/alex/anaconda3/bin/teLeap: Warning!
There are missing parameters.
Unit is OK.
Loading parameters: ./lig.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
Creating lig.lib
Building topology.
Building atom parameters.
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
/home/alex/anaconda3/bin/teLeap: Note.
1-4: angle 17 19 duplicates bond ('triangular' bond) or angle ('square'
bond)
/home/alex/anaconda3/bin/teLeap: Note.
1-4: angle 17 18 duplicates bond ('triangular' bond) or angle ('square'
bond)
/home/alex/anaconda3/bin/teLeap: Note.
1-4: angle 18 19 duplicates bond ('triangular' bond) or angle ('square'
bond)
Building improper torsion parameters.
total 8 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
LIG 1
)
(no restraints)
Quit
Exiting LEaP: Errors = 10; Warnings = 1; Notes = 3.
On Thu, Dec 3, 2020 at 5:45 AM David A Case <david.case.rutgers.edu> wrote:
> On Wed, Dec 02, 2020, Alexander Izvorski wrote:
> >
> >I'm trying to figure out how to use GAFF2 in antechamber/tleap.
> >
> >antechamber -i lig_in.mol2 -fi mol2 -o lig.mol2 -fo mol2 -c bcc -s 2 -rn
> LIG
> >
> >I noticed that "-at gaff2" is a possible option here - is it needed?
>
> Yes.
>
> >what happens is a bunch of errors when running tleap later,
> >"Error! Could not find bond parameter for: ns - ca" and similar
>
> Can you provide a small example that shows this error?
>
> >2. Run parmchk: "-s gaff2" enables GAFF2 here
> >3. Run tleap: source leaprc.gaff2 loads GAFF2
> >
>
> Above are correct.
>
> >This works using sustiva.mol2
>
> Since it works for sustiva, we would need to see the case that fails. I
> use gaff2 a lot, and have not seen the problem you describe.
>
> ...thanks...dave
>
> cc-ing to junmei: can't we finally make gaff2 the default? I suspect
> tons of people are still using gaff1 because one needs to make three
> different changes.
>
>
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Received on Thu Dec 03 2020 - 22:30:02 PST
