*Interestingly, I don't see an error with the mother compound at this
moment, *
$antechamber -i furazan.mol2 -fi mol2 -o furazan.prepc -fo prepc -nc -0 -c
bcc -s 2 -at gaff2
Welcome to antechamber 17.3: molecular input file processor.
acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for mol2 File --
Status: pass
Info: Finished reading file (furazan.mol2).
-- Check Unusual Elements --
Status: pass
-- Check Open Valences --
Warning: The number of bonds (3) for atom (ID: 2, Name: N1) does not match
the connectivity (4) for atom type (N.4) defined in
CORR_NAME_TYPE.DAT.
Warning: The number of bonds (3) for atom (ID: 3, Name: N2) does not match
the connectivity (4) for atom type (N.4) defined in
CORR_NAME_TYPE.DAT.
But, you may safely ignore the warnings if your molecule
uses atom names or element names as atom types.
-- 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/amber18/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac
Running: /home/amber18/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff2
Info: Total number of electrons: 38; net charge: 0
Running: /home/amber18/bin/sqm -O -i sqm.in -o sqm.out
Running: /home/amber18/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o
ANTECHAMBER_AM1BCC.AC -f ac -p /home/amber18/dat/antechamber/BCCPARM.DAT -s
2 -j 1
Running: /home/amber18/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC
-i ANTECHAMBER_AM1BCC_PRE.AC
Running: /home/amber18/bin/prepgen -i ANTECHAMBER_PREP.AC -f car -o
furazan.prepc -rn "UNL" -rf molecule.res
$ ls
ANTECHAMBER_AC.AC ANTECHAMBER_AM1BCC_PRE.AC ANTECHAMBER_PREP.AC
furazan.mol2
PREP.INF sqm.pdb
ANTECHAMBER_AC.AC0 ANTECHAMBER_BOND_TYPE.AC ANTECHAMBER_PREP.AC0
furazan.prepc sqm.in
ANTECHAMBER_AM1BCC.AC ANTECHAMBER_BOND_TYPE.AC0 ATOMTYPE.INF
NEWPDB.PDB
sqm.out
$
$ parmchk2 -i furazan.prepc -f prepc -o furazan.frcmod -a Y
$ ls
ANTECHAMBER_AC.AC ANTECHAMBER_BOND_TYPE.AC ANTECHAMBER_PREP.AC0
furazan.prepc sqm.out
ANTECHAMBER_AC.AC0 ANTECHAMBER_BOND_TYPE.AC0 ATOMTYPE.INF
NEWPDB.PDB
sqm.pdb
ANTECHAMBER_AM1BCC.AC ANTECHAMBER.FRCMOD furazan.frcmod
PREP.INF
ANTECHAMBER_AM1BCC_PRE.AC ANTECHAMBER_PREP.AC furazan.mol2
sqm.in
$ ls
*But my modified compound did have the error:*
$ antechamber -i st0.mol2 -fi mol2 -o st0.prepc -fo prepc -nc -0 -c bcc -s
2 -at gaff2
Welcome to antechamber 17.3: molecular input file processor.
acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for mol2 File --
Status: pass
Info: Finished reading file (st0.mol2).
-- Check Unusual Elements --
Status: pass
-- Check Open Valences --
Status: pass
-- Check Geometry --
for those bonded
for those not bonded
Status: pass
-- Check Weird Bonds --
/home/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
Weird atomic valence (3) for atom (ID: 7, Name: O1).
Please check atomic connectivity.
*So I added "-dr no" in my antechamber, and it worked fine.*
$ antechamber -i st0.mol2 -fi mol2 -o st0.prepc -fo prepc -nc -0 -c bcc -s
2 -at gaff2 *-dr no*
Welcome to antechamber 17.3: molecular input file processor.
Info: Finished reading file (st0.mol2).
Running: /home/amber18/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac
Running: /home/amber18/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff2
Info: Total number of electrons: 154; net charge: 0
Running: /home/amber18/bin/sqm -O -i sqm.in -o sqm.out
Running: /home/amber18/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o
ANTECHAMBER_AM1BCC.AC -f ac -p /home/amber18/dat/antechamber/BCCPARM.DAT -s
2 -j 1
Running: /home/amber18/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC
-i ANTECHAMBER_AM1BCC_PRE.AC
Running: /home/amber18/bin/prepgen -i ANTECHAMBER_PREP.AC -f car -o
st0.prepc -rn "ST0" -rf molecule.res
$ parmchk2 -i st0.prepc -f prepc -o st0.frcmod -a Y
$ ls
On Tue, May 19, 2020 at 5:03 AM David A Case <david.case.rutgers.edu> wrote:
> On Sat, May 16, 2020, Lod King wrote:
>
> >Sorry that I did not attach the file, here it is the furazan molecule in
> >mol2.
>
> I can't reproduce any problem here, with this antechamber run:
>
> antechamber -fi mol2 -i furazan.mol2 -fo mol2 -o foo.mol2
>
> Here is output:
>
>
> ----------------------------------------------------------------------------
> 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
> -- Check Unusual Elements --
> Status: pass
> -- Check Open Valences --
> Warning: The number of bonds (3) for atom (ID: 2, Name: N) does not match
> the connectivity (4) for atom type (N.4) defined in
> CORR_NAME_TYPE.DAT.
> Warning: The number of bonds (3) for atom (ID: 3, Name: N1) does not match
> the connectivity (4) for atom type (N.4) defined in
> CORR_NAME_TYPE.DAT.
> But, you may safely ignore the warnings if your molecule
> uses atom names or element names as atom types.
> -- 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.
>
> ----------------------------------------------------------------------------
>
> I've attached the output mol2 file (with gaff atom types).
>
> So: what version of AmberTools are you using? Are you doing what I
> outlined above? It seems possible that having the N atoms identified as
> N.4 could cause a problem, but I'm not seeing it.
>
> If you can't get things to work, we will need *full* details of exactly
> what was done, in order to try to reproduce the behavior you see.
>
> ....dac
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue May 19 2020 - 11:00:01 PDT
