P.S. Just now I noticed that the errors happen before loading lig.frcmod,
so I tried loading that first, and the errors disappeared. Hmm, so maybe
it was just the load order - " loadamberparams lig.frcmod" should be before
"loadmol2 lig.mol2"?
With this tleap.in
source leaprc.protein.ff14SB
source leaprc.water.tip3p
source leaprc.gaff2
loadamberparams lig.frcmod
LIG = loadmol2 lig.mol2
check LIG
saveoff LIG lig.lib
saveamberparm LIG lig.prmtop lig.inpcrd
quit
the results are:
$ 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 parameters: ./lig.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
Loading Mol2 file: ./lig.mol2
Reading MOLECULE named LIG
Checking 'LIG'....
Checking parameters for unit 'LIG'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
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 = 0; Warnings = 0; Notes = 3.
On Thu, Dec 3, 2020 at 10:11 PM Alexander Izvorski <aizvorski.gmail.com>
wrote:
> 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.
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Thu Dec 03 2020 - 22:30:02 PST
